2023-09-12T10:47:51,294 Created temporary directory: /tmp/pip-build-tracker-xeyiwt3d 2023-09-12T10:47:51,295 Initialized build tracking at /tmp/pip-build-tracker-xeyiwt3d 2023-09-12T10:47:51,295 Created build tracker: /tmp/pip-build-tracker-xeyiwt3d 2023-09-12T10:47:51,296 Entered build tracker: /tmp/pip-build-tracker-xeyiwt3d 2023-09-12T10:47:51,297 Created temporary directory: /tmp/pip-wheel-wbntdows 2023-09-12T10:47:51,300 Created temporary directory: /tmp/pip-ephem-wheel-cache-c5h6d1gr 2023-09-12T10:47:51,321 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-12T10:47:51,325 2 location(s) to search for versions of maagbel: 2023-09-12T10:47:51,325 * https://pypi.org/simple/maagbel/ 2023-09-12T10:47:51,325 * https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:47:51,326 Fetching project page and analyzing links: https://pypi.org/simple/maagbel/ 2023-09-12T10:47:51,326 Getting page https://pypi.org/simple/maagbel/ 2023-09-12T10:47:51,328 Found index url https://pypi.org/simple/ 2023-09-12T10:47:51,467 Fetched page https://pypi.org/simple/maagbel/ as application/vnd.pypi.simple.v1+json 2023-09-12T10:47:51,469 Found link https://files.pythonhosted.org/packages/66/de/8fe70531b8e76dcc8f1208ab3bee0fe940b515b9c5b2bf66832f627331c9/maagbel-0.1.1.tar.gz (from https://pypi.org/simple/maagbel/), version: 0.1.1 2023-09-12T10:47:51,470 Found link https://files.pythonhosted.org/packages/56/df/95416ae78c46c743df0739d430805645965f57b4cee30083ac8ff9c1ece7/maagbel-0.1.2.tar.gz (from https://pypi.org/simple/maagbel/), version: 0.1.2 2023-09-12T10:47:51,470 Fetching project page and analyzing links: https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:47:51,471 Getting page https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:47:51,472 Found index url https://www.piwheels.org/simple/ 2023-09-12T10:47:51,744 Fetched page https://www.piwheels.org/simple/maagbel/ as text/html 2023-09-12T10:47:51,745 Skipping link: not a file: https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:47:51,746 Skipping link: not a file: https://pypi.org/simple/maagbel/ 2023-09-12T10:47:51,764 Given no hashes to check 1 links for project 'maagbel': discarding no candidates 2023-09-12T10:47:51,782 Collecting maagbel==0.1.2 2023-09-12T10:47:51,785 Created temporary directory: /tmp/pip-unpack-8gafzzdo 2023-09-12T10:47:52,005 Downloading maagbel-0.1.2.tar.gz (1.8 MB) 2023-09-12T10:47:53,316 Added maagbel==0.1.2 from https://files.pythonhosted.org/packages/56/df/95416ae78c46c743df0739d430805645965f57b4cee30083ac8ff9c1ece7/maagbel-0.1.2.tar.gz to build tracker '/tmp/pip-build-tracker-xeyiwt3d' 2023-09-12T10:47:53,318 Running setup.py (path:/tmp/pip-wheel-wbntdows/maagbel_aac4441a813c4a88b1e338f5f0615037/setup.py) egg_info for package maagbel 2023-09-12T10:47:53,319 Created temporary directory: /tmp/pip-pip-egg-info-t171rlk3 2023-09-12T10:47:53,320 Preparing metadata (setup.py): started 2023-09-12T10:47:53,321 Running command python setup.py egg_info 2023-09-12T10:47:53,855 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'mail' 2023-09-12T10:47:53,856 warnings.warn(msg) 2023-09-12T10:47:54,408 running egg_info 2023-09-12T10:47:54,410 creating /tmp/pip-pip-egg-info-t171rlk3/maagbel.egg-info 2023-09-12T10:47:54,434 writing /tmp/pip-pip-egg-info-t171rlk3/maagbel.egg-info/PKG-INFO 2023-09-12T10:47:54,437 writing dependency_links to /tmp/pip-pip-egg-info-t171rlk3/maagbel.egg-info/dependency_links.txt 2023-09-12T10:47:54,440 writing top-level names to /tmp/pip-pip-egg-info-t171rlk3/maagbel.egg-info/top_level.txt 2023-09-12T10:47:54,441 writing manifest file '/tmp/pip-pip-egg-info-t171rlk3/maagbel.egg-info/SOURCES.txt' 2023-09-12T10:47:54,525 reading manifest file '/tmp/pip-pip-egg-info-t171rlk3/maagbel.egg-info/SOURCES.txt' 2023-09-12T10:47:54,527 reading manifest template 'MANIFEST.in' 2023-09-12T10:47:54,551 writing manifest file '/tmp/pip-pip-egg-info-t171rlk3/maagbel.egg-info/SOURCES.txt' 2023-09-12T10:47:54,661 Preparing metadata (setup.py): finished with status 'done' 2023-09-12T10:47:54,665 Source in /tmp/pip-wheel-wbntdows/maagbel_aac4441a813c4a88b1e338f5f0615037 has version 0.1.2, which satisfies requirement maagbel==0.1.2 from https://files.pythonhosted.org/packages/56/df/95416ae78c46c743df0739d430805645965f57b4cee30083ac8ff9c1ece7/maagbel-0.1.2.tar.gz 2023-09-12T10:47:54,666 Removed maagbel==0.1.2 from https://files.pythonhosted.org/packages/56/df/95416ae78c46c743df0739d430805645965f57b4cee30083ac8ff9c1ece7/maagbel-0.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-xeyiwt3d' 2023-09-12T10:47:54,670 Created temporary directory: /tmp/pip-unpack-xd_pa0yd 2023-09-12T10:47:54,671 Created temporary directory: /tmp/pip-unpack-61yukkdq 2023-09-12T10:47:54,674 Building wheels for collected packages: maagbel 2023-09-12T10:47:54,678 Created temporary directory: /tmp/pip-wheel-1p0xjpov 2023-09-12T10:47:54,678 Building wheel for maagbel (setup.py): started 2023-09-12T10:47:54,680 Destination directory: /tmp/pip-wheel-1p0xjpov 2023-09-12T10:47:54,680 Running command python setup.py bdist_wheel 2023-09-12T10:47:55,181 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'mail' 2023-09-12T10:47:55,182 warnings.warn(msg) 2023-09-12T10:47:55,720 running bdist_wheel 2023-09-12T10:47:55,790 running build 2023-09-12T10:47:55,790 running build_ext 2023-09-12T10:47:56,297 building 'maagbel._cpp' extension 2023-09-12T10:47:56,298 swigging maagbel/cpp.i to maagbel/cpp_wrap.cpp 2023-09-12T10:47:56,298 swig -python -c++ -Iinclude -o maagbel/cpp_wrap.cpp maagbel/cpp.i 2023-09-12T10:47:58,662 include/openbabel/obconversion.h:369: Warning 325: Nested struct not currently supported (StreamState ignored) 2023-09-12T10:47:59,475 include/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored) 2023-09-12T10:47:59,682 include/openbabel/spectrophore.h:571: Warning 312: Nested struct not currently supported (ignored). 2023-09-12T10:47:59,684 include/openbabel/spectrophore.h:578: Warning 312: Nested struct not currently supported (ignored). 2023-09-12T10:48:21,149 creating build 2023-09-12T10:48:21,150 creating build/temp.linux-armv7l-cpython-311 2023-09-12T10:48:21,151 creating build/temp.linux-armv7l-cpython-311/src 2023-09-12T10:48:21,152 creating build/temp.linux-armv7l-cpython-311/src/charges 2023-09-12T10:48:21,153 creating build/temp.linux-armv7l-cpython-311/src/depict 2023-09-12T10:48:21,154 creating build/temp.linux-armv7l-cpython-311/src/descriptors 2023-09-12T10:48:21,155 creating build/temp.linux-armv7l-cpython-311/src/fingerprints 2023-09-12T10:48:21,156 creating build/temp.linux-armv7l-cpython-311/src/forcefields 2023-09-12T10:48:21,157 creating build/temp.linux-armv7l-cpython-311/src/formats 2023-09-12T10:48:21,160 creating build/temp.linux-armv7l-cpython-311/src/math 2023-09-12T10:48:21,161 creating build/temp.linux-armv7l-cpython-311/src/ops 2023-09-12T10:48:21,163 creating build/temp.linux-armv7l-cpython-311/src/stereo 2023-09-12T10:48:21,164 creating build/temp.linux-armv7l-cpython-311/maagbel 2023-09-12T10:48:21,164 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/aggregate.cpp -o build/temp.linux-armv7l-cpython-311/./src/aggregate.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:48:21,170 Using built-in specs. 2023-09-12T10:48:21,171 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:21,171 Target: arm-linux-gnueabihf 2023-09-12T10:48:21,172 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:48:21,172 Thread model: posix 2023-09-12T10:48:21,173 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:21,174 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:21,174 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/aggregate.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:21,175 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/aggregate.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase aggregate.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccjTF10g.s 2023-09-12T10:48:21,185 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:21,186 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:21,187 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:21,187 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:21,188 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:21,189 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:21,189 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:21,190 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:21,190 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:21,190 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:21,191 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:21,192 #include "..." search starts here: 2023-09-12T10:48:21,192 #include <...> search starts here: 2023-09-12T10:48:21,193 /usr/include/eigen3 2023-09-12T10:48:21,193 include 2023-09-12T10:48:21,194 /usr/include/python3.11 2023-09-12T10:48:21,194 /usr/include/c++/12 2023-09-12T10:48:21,195 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:21,195 /usr/include/c++/12/backward 2023-09-12T10:48:21,196 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:21,196 /usr/local/include 2023-09-12T10:48:21,197 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:21,198 /usr/include 2023-09-12T10:48:21,198 End of search list. 2023-09-12T10:48:21,199 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:21,199 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:21,201 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:21,201 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:21,213 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:22,827 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:22,828 from include/openbabel/mol.h:43, 2023-09-12T10:48:22,829 from ./src/aggregate.cpp:20: 2023-09-12T10:48:22,829 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:22,830 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:22,830 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:22,831 | ^ 2023-09-12T10:48:22,831 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:22,832 37 | # define UNUSED(x) x 2023-09-12T10:48:22,833 | ^ 2023-09-12T10:48:23,599 In file included from include/openbabel/mol.h:52: 2023-09-12T10:48:23,600 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:23,600 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:23,601 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:23,601 | ^ 2023-09-12T10:48:23,602 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:23,602 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:23,603 | ^~~~~~~~ 2023-09-12T10:48:23,607 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:23,607 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:23,608 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:23,609 | ^ 2023-09-12T10:48:23,610 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:23,610 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:23,611 | ^~~~~~~~ 2023-09-12T10:48:23,628 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:23,629 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:23,630 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:23,630 | ^ 2023-09-12T10:48:23,631 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:23,632 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:23,632 | ^~~~~~~~ 2023-09-12T10:48:23,637 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:23,638 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:23,639 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:23,639 | ^ 2023-09-12T10:48:23,640 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:23,640 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:23,641 | ^~~~~~~~ 2023-09-12T10:48:23,857 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:48:23,858 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:48:23,858 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:48:23,859 | ^ 2023-09-12T10:48:23,860 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:23,860 37 | # define UNUSED(x) x 2023-09-12T10:48:23,861 | ^ 2023-09-12T10:48:23,861 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:48:23,862 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:48:23,862 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:48:23,863 | ^ 2023-09-12T10:48:23,863 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:23,864 37 | # define UNUSED(x) x 2023-09-12T10:48:23,865 | ^ 2023-09-12T10:48:24,200 ./src/aggregate.cpp: In member function ‘float OpenBabel::OBAggregate::MinVDWDist(bool, double)’: 2023-09-12T10:48:24,200 ./src/aggregate.cpp:151:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:48:24,201 151 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2023-09-12T10:48:24,201 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:24,202 ./src/aggregate.cpp:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:48:24,203 156 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2023-09-12T10:48:24,204 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:24,212 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’: 2023-09-12T10:48:24,213 ./src/aggregate.cpp:245:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:48:24,213 245 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2023-09-12T10:48:24,214 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:24,234 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::FindAllConnections(bool)’: 2023-09-12T10:48:24,235 ./src/aggregate.cpp:316:20: warning: unused variable ‘a’ [-Wunused-variable] 2023-09-12T10:48:24,236 316 | OBAtom *atom, *a; 2023-09-12T10:48:24,236 | ^ 2023-09-12T10:48:24,258 ./src/aggregate.cpp: In member function ‘std::string OpenBabel::OBAggregate::GetConnections()’: 2023-09-12T10:48:24,259 ./src/aggregate.cpp:558:13: warning: unused variable ‘id’ [-Wunused-variable] 2023-09-12T10:48:24,259 558 | int id = -1; 2023-09-12T10:48:24,261 | ^~ 2023-09-12T10:48:24,261 ./src/aggregate.cpp:559:13: warning: unused variable ‘elements’ [-Wunused-variable] 2023-09-12T10:48:24,262 559 | int elements = 0; 2023-09-12T10:48:24,262 | ^~~~~~~~ 2023-09-12T10:48:24,265 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::PrintConnections()’: 2023-09-12T10:48:24,266 ./src/aggregate.cpp:584:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:48:24,266 584 | if ( atom->GetIdx() != id+1 ){ 2023-09-12T10:48:24,267 | ~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T10:48:24,292 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::AddToTag(int, int)’: 2023-09-12T10:48:24,293 ./src/aggregate.cpp:772:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:48:24,295 772 | if (tag >= _molTags.size() || tag<0){ 2023-09-12T10:48:24,296 | ~~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:29,382 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:48:29,383 from include/openbabel/mol.h:35: 2023-09-12T10:48:29,384 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:48:29,384 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:48:29,385 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:48:29,385 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,476 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:48:30,477 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:48:30,477 inlined from ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’ at ./src/aggregate.cpp:244:29: 2023-09-12T10:48:30,478 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:48:30,479 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:48:30,480 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,480 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:48:30,481 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:48:30,482 inlined from ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’ at ./src/aggregate.cpp:246:31: 2023-09-12T10:48:30,482 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:48:30,483 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:48:30,483 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:32,138 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/aggregate.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:32,138 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/aggregate.o /tmp/ccjTF10g.s 2023-09-12T10:48:32,145 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:32,676 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:48:32,677 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:48:32,677 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/aggregate.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/aggregate.' 2023-09-12T10:48:32,680 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/alias.cpp -o build/temp.linux-armv7l-cpython-311/./src/alias.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:48:32,684 Using built-in specs. 2023-09-12T10:48:32,686 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:32,686 Target: arm-linux-gnueabihf 2023-09-12T10:48:32,687 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:48:32,687 Thread model: posix 2023-09-12T10:48:32,688 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:32,688 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:32,689 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/alias.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:32,690 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/alias.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase alias.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccptXpiX.s 2023-09-12T10:48:32,697 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:32,698 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:32,699 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:32,700 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:32,700 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:32,700 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:32,701 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:32,701 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:32,702 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:32,702 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:32,703 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:32,704 #include "..." search starts here: 2023-09-12T10:48:32,704 #include <...> search starts here: 2023-09-12T10:48:32,705 /usr/include/eigen3 2023-09-12T10:48:32,705 include 2023-09-12T10:48:32,706 /usr/include/python3.11 2023-09-12T10:48:32,707 /usr/include/c++/12 2023-09-12T10:48:32,707 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:32,708 /usr/include/c++/12/backward 2023-09-12T10:48:32,709 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:32,709 /usr/local/include 2023-09-12T10:48:32,710 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:32,710 /usr/include 2023-09-12T10:48:32,711 End of search list. 2023-09-12T10:48:32,711 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:32,712 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:32,713 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:32,714 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:32,717 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:34,466 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:34,467 from include/openbabel/mol.h:43, 2023-09-12T10:48:34,468 from include/openbabel/alias.h:20, 2023-09-12T10:48:34,468 from ./src/alias.cpp:17: 2023-09-12T10:48:34,469 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:34,470 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:34,470 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:34,471 | ^ 2023-09-12T10:48:34,472 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:34,472 37 | # define UNUSED(x) x 2023-09-12T10:48:34,473 | ^ 2023-09-12T10:48:35,241 In file included from include/openbabel/mol.h:52: 2023-09-12T10:48:35,242 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:35,243 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:35,243 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:35,244 | ^ 2023-09-12T10:48:35,245 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:35,245 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:35,246 | ^~~~~~~~ 2023-09-12T10:48:35,247 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:35,248 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:35,248 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:35,249 | ^ 2023-09-12T10:48:35,249 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:35,250 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:35,251 | ^~~~~~~~ 2023-09-12T10:48:35,267 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:35,267 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:35,268 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:35,269 | ^ 2023-09-12T10:48:35,269 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:35,270 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:35,271 | ^~~~~~~~ 2023-09-12T10:48:35,273 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:35,274 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:35,275 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:35,275 | ^ 2023-09-12T10:48:35,276 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:35,277 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:35,277 | ^~~~~~~~ 2023-09-12T10:48:35,487 In file included from include/openbabel/format.h:22, 2023-09-12T10:48:35,488 from include/openbabel/obconversion.h:37, 2023-09-12T10:48:35,488 from ./src/alias.cpp:18: 2023-09-12T10:48:35,489 include/openbabel/plugin.h: At global scope: 2023-09-12T10:48:35,490 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:48:35,490 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:48:35,491 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:35,492 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:48:35,492 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:48:35,493 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:48:35,493 from /usr/include/c++/12/ios:42, 2023-09-12T10:48:35,494 from /usr/include/c++/12/istream:38, 2023-09-12T10:48:35,494 from /usr/include/c++/12/sstream:38, 2023-09-12T10:48:35,495 from ./src/alias.cpp:15: 2023-09-12T10:48:35,495 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:48:35,496 131 | struct binary_function 2023-09-12T10:48:35,497 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:40,647 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/alias.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:40,648 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/alias.o /tmp/ccptXpiX.s 2023-09-12T10:48:40,652 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:40,999 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:48:41,000 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:48:41,000 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/alias.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/alias.' 2023-09-12T10:48:41,002 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/atom.cpp -o build/temp.linux-armv7l-cpython-311/./src/atom.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:48:41,006 Using built-in specs. 2023-09-12T10:48:41,007 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:41,008 Target: arm-linux-gnueabihf 2023-09-12T10:48:41,008 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:48:41,009 Thread model: posix 2023-09-12T10:48:41,009 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:41,010 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:41,010 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/atom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:41,011 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/atom.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase atom.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccE6W6Nx.s 2023-09-12T10:48:41,020 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:41,021 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:41,022 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:41,023 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:41,023 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:41,024 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:41,024 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:41,025 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:41,026 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:41,027 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:41,027 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:41,028 #include "..." search starts here: 2023-09-12T10:48:41,028 #include <...> search starts here: 2023-09-12T10:48:41,029 /usr/include/eigen3 2023-09-12T10:48:41,029 include 2023-09-12T10:48:41,030 /usr/include/python3.11 2023-09-12T10:48:41,030 /usr/include/c++/12 2023-09-12T10:48:41,031 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:41,031 /usr/include/c++/12/backward 2023-09-12T10:48:41,032 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:41,033 /usr/local/include 2023-09-12T10:48:41,033 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:41,034 /usr/include 2023-09-12T10:48:41,035 End of search list. 2023-09-12T10:48:41,035 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:41,036 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:41,038 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:41,038 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:41,042 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:42,512 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:42,513 from ./src/atom.cpp:22: 2023-09-12T10:48:42,513 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:42,514 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:42,514 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:42,515 | ^ 2023-09-12T10:48:42,515 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:42,516 37 | # define UNUSED(x) x 2023-09-12T10:48:42,516 | ^ 2023-09-12T10:48:43,361 In file included from include/openbabel/mol.h:52, 2023-09-12T10:48:43,362 from include/openbabel/isomorphism.h:27, 2023-09-12T10:48:43,363 from include/openbabel/stereo/stereo.h:28, 2023-09-12T10:48:43,363 from ./src/atom.cpp:23: 2023-09-12T10:48:43,364 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:43,364 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:43,365 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:43,365 | ^ 2023-09-12T10:48:43,366 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:43,367 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:43,367 | ^~~~~~~~ 2023-09-12T10:48:43,369 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:43,369 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:43,370 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:43,371 | ^ 2023-09-12T10:48:43,371 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:43,372 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:43,373 | ^~~~~~~~ 2023-09-12T10:48:43,389 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:43,390 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:43,390 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:43,391 | ^ 2023-09-12T10:48:43,392 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:43,392 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:43,393 | ^~~~~~~~ 2023-09-12T10:48:43,397 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:43,397 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:43,398 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:43,398 | ^ 2023-09-12T10:48:43,399 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:43,399 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:43,400 | ^~~~~~~~ 2023-09-12T10:48:43,765 ./src/atom.cpp: In member function ‘int OpenBabel::OBAtom::HighestBondOrder()’: 2023-09-12T10:48:43,766 ./src/atom.cpp:302:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:48:43,766 302 | if(bond->GetBO() > highest) 2023-09-12T10:48:43,767 | ~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T10:48:50,196 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/atom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:50,196 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/atom.o /tmp/ccE6W6Nx.s 2023-09-12T10:48:50,201 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:50,649 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:48:50,650 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:48:50,650 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/atom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/atom.' 2023-09-12T10:48:50,652 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/base.cpp -o build/temp.linux-armv7l-cpython-311/./src/base.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:48:50,656 Using built-in specs. 2023-09-12T10:48:50,657 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:50,658 Target: arm-linux-gnueabihf 2023-09-12T10:48:50,659 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:48:50,659 Thread model: posix 2023-09-12T10:48:50,660 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:50,660 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:50,661 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/base.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:50,661 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/base.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase base.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccqOXnba.s 2023-09-12T10:48:50,670 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:50,670 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:50,671 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:50,672 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:50,673 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:50,673 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:50,674 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:50,675 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:50,675 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:50,676 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:50,676 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:50,677 #include "..." search starts here: 2023-09-12T10:48:50,677 #include <...> search starts here: 2023-09-12T10:48:50,678 /usr/include/eigen3 2023-09-12T10:48:50,679 include 2023-09-12T10:48:50,679 /usr/include/python3.11 2023-09-12T10:48:50,680 /usr/include/c++/12 2023-09-12T10:48:50,681 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:50,681 /usr/include/c++/12/backward 2023-09-12T10:48:50,682 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:50,683 /usr/local/include 2023-09-12T10:48:50,684 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:50,684 /usr/include 2023-09-12T10:48:50,684 End of search list. 2023-09-12T10:48:50,685 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:50,685 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:50,686 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:50,687 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:50,689 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:52,039 In file included from ./src/base.cpp:21: 2023-09-12T10:48:52,039 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:52,040 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:52,041 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:52,041 | ^ 2023-09-12T10:48:52,042 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:52,042 37 | # define UNUSED(x) x 2023-09-12T10:48:52,043 | ^ 2023-09-12T10:48:53,269 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/base.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:53,270 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/base.o /tmp/ccqOXnba.s 2023-09-12T10:48:53,274 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:53,377 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:48:53,377 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:48:53,378 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/base.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/base.' 2023-09-12T10:48:53,379 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/bitvec.cpp -o build/temp.linux-armv7l-cpython-311/./src/bitvec.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:48:53,383 Using built-in specs. 2023-09-12T10:48:53,384 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:53,384 Target: arm-linux-gnueabihf 2023-09-12T10:48:53,385 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:48:53,386 Thread model: posix 2023-09-12T10:48:53,386 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:53,386 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:53,387 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bitvec.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:53,387 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/bitvec.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase bitvec.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc1uNmNN.s 2023-09-12T10:48:53,396 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:53,397 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:53,398 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:53,398 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:53,399 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:53,399 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:53,400 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:53,400 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:53,401 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:53,402 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:53,402 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:53,403 #include "..." search starts here: 2023-09-12T10:48:53,403 #include <...> search starts here: 2023-09-12T10:48:53,404 /usr/include/eigen3 2023-09-12T10:48:53,404 include 2023-09-12T10:48:53,405 /usr/include/python3.11 2023-09-12T10:48:53,405 /usr/include/c++/12 2023-09-12T10:48:53,406 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:53,406 /usr/include/c++/12/backward 2023-09-12T10:48:53,407 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:53,408 /usr/local/include 2023-09-12T10:48:53,408 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:53,409 /usr/include 2023-09-12T10:48:53,409 End of search list. 2023-09-12T10:48:53,410 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:53,410 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:53,411 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:53,412 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:53,414 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:57,694 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bitvec.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:57,694 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/bitvec.o /tmp/cc1uNmNN.s 2023-09-12T10:48:57,700 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:57,941 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:48:57,942 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:48:57,942 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bitvec.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/bitvec.' 2023-09-12T10:48:57,943 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/bond.cpp -o build/temp.linux-armv7l-cpython-311/./src/bond.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:48:57,948 Using built-in specs. 2023-09-12T10:48:57,948 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:57,949 Target: arm-linux-gnueabihf 2023-09-12T10:48:57,950 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:48:57,950 Thread model: posix 2023-09-12T10:48:57,951 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:57,951 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:57,952 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bond.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:48:57,952 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/bond.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase bond.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccJNl4ap.s 2023-09-12T10:48:57,960 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:57,961 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:57,962 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:57,963 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:57,963 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:57,964 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:57,965 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:57,965 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:57,966 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:57,966 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:57,967 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:57,967 #include "..." search starts here: 2023-09-12T10:48:57,968 #include <...> search starts here: 2023-09-12T10:48:57,969 /usr/include/eigen3 2023-09-12T10:48:57,969 include 2023-09-12T10:48:57,970 /usr/include/python3.11 2023-09-12T10:48:57,970 /usr/include/c++/12 2023-09-12T10:48:57,971 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:57,971 /usr/include/c++/12/backward 2023-09-12T10:48:57,972 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:57,973 /usr/local/include 2023-09-12T10:48:57,973 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:57,974 /usr/include 2023-09-12T10:48:57,974 End of search list. 2023-09-12T10:48:57,975 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:57,975 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:57,977 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:57,977 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:57,978 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:59,655 In file included from include/openbabel/bond.h:31, 2023-09-12T10:48:59,656 from ./src/bond.cpp:21: 2023-09-12T10:48:59,657 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:59,658 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:59,659 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:59,659 | ^ 2023-09-12T10:48:59,660 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:59,660 37 | # define UNUSED(x) x 2023-09-12T10:48:59,661 | ^ 2023-09-12T10:49:00,506 In file included from include/openbabel/mol.h:52, 2023-09-12T10:49:00,506 from ./src/bond.cpp:22: 2023-09-12T10:49:00,507 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:00,508 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:00,508 862 | {return new OBVibrationData(*this);} 2023-09-12T10:49:00,509 | ^ 2023-09-12T10:49:00,509 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:49:00,510 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:49:00,511 | ^~~~~~~~ 2023-09-12T10:49:00,512 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:00,513 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:00,513 907 | {return new OBDOSData(*this);} 2023-09-12T10:49:00,514 | ^ 2023-09-12T10:49:00,515 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:49:00,516 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:49:00,517 | ^~~~~~~~ 2023-09-12T10:49:00,530 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:00,531 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:00,532 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:49:00,532 | ^ 2023-09-12T10:49:00,533 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:49:00,534 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:49:00,534 | ^~~~~~~~ 2023-09-12T10:49:00,537 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:00,537 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:00,538 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:49:00,539 | ^ 2023-09-12T10:49:00,539 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:49:00,540 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:49:00,541 | ^~~~~~~~ 2023-09-12T10:49:03,605 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bond.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:03,606 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/bond.o /tmp/ccJNl4ap.s 2023-09-12T10:49:03,611 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:49:03,796 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:49:03,796 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:49:03,797 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bond.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/bond.' 2023-09-12T10:49:03,798 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/bondtyper.cpp -o build/temp.linux-armv7l-cpython-311/./src/bondtyper.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:49:03,802 Using built-in specs. 2023-09-12T10:49:03,803 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:49:03,804 Target: arm-linux-gnueabihf 2023-09-12T10:49:03,805 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:49:03,805 Thread model: posix 2023-09-12T10:49:03,806 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:49:03,806 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:49:03,807 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bondtyper.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:03,807 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/bondtyper.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase bondtyper.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccjhqZHd.s 2023-09-12T10:49:03,815 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:03,816 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:03,817 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:03,818 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:03,818 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:49:03,819 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:49:03,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:49:03,820 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:49:03,821 ignoring duplicate directory "/usr/include/" 2023-09-12T10:49:03,821 as it is a non-system directory that duplicates a system directory 2023-09-12T10:49:03,822 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:49:03,823 #include "..." search starts here: 2023-09-12T10:49:03,823 #include <...> search starts here: 2023-09-12T10:49:03,824 /usr/include/eigen3 2023-09-12T10:49:03,824 include 2023-09-12T10:49:03,825 /usr/include/python3.11 2023-09-12T10:49:03,825 /usr/include/c++/12 2023-09-12T10:49:03,826 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:49:03,826 /usr/include/c++/12/backward 2023-09-12T10:49:03,827 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:49:03,827 /usr/local/include 2023-09-12T10:49:03,828 /usr/include/arm-linux-gnueabihf 2023-09-12T10:49:03,829 /usr/include 2023-09-12T10:49:03,829 End of search list. 2023-09-12T10:49:03,830 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:03,830 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:03,831 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:03,832 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:03,834 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:49:05,391 In file included from include/openbabel/atom.h:33, 2023-09-12T10:49:05,392 from include/openbabel/mol.h:43, 2023-09-12T10:49:05,393 from ./src/bondtyper.cpp:20: 2023-09-12T10:49:05,393 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:49:05,394 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:49:05,395 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:49:05,396 | ^ 2023-09-12T10:49:05,396 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:49:05,397 37 | # define UNUSED(x) x 2023-09-12T10:49:05,397 | ^ 2023-09-12T10:49:06,162 In file included from include/openbabel/mol.h:52: 2023-09-12T10:49:06,162 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:06,163 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:06,163 862 | {return new OBVibrationData(*this);} 2023-09-12T10:49:06,164 | ^ 2023-09-12T10:49:06,164 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:49:06,165 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:49:06,166 | ^~~~~~~~ 2023-09-12T10:49:06,167 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:06,167 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:06,168 907 | {return new OBDOSData(*this);} 2023-09-12T10:49:06,169 | ^ 2023-09-12T10:49:06,170 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:49:06,170 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:49:06,171 | ^~~~~~~~ 2023-09-12T10:49:06,186 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:06,187 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:06,188 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:49:06,188 | ^ 2023-09-12T10:49:06,189 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:49:06,190 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:49:06,190 | ^~~~~~~~ 2023-09-12T10:49:06,192 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:06,193 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:06,194 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:49:06,195 | ^ 2023-09-12T10:49:06,196 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:49:06,197 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:49:06,198 | ^~~~~~~~ 2023-09-12T10:49:09,676 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bondtyper.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:09,676 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/bondtyper.o /tmp/ccjhqZHd.s 2023-09-12T10:49:09,681 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:49:09,892 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:49:09,893 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:49:09,894 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/bondtyper.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/bondtyper.' 2023-09-12T10:49:09,895 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/builder.cpp -o build/temp.linux-armv7l-cpython-311/./src/builder.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:49:09,899 Using built-in specs. 2023-09-12T10:49:09,900 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:49:09,900 Target: arm-linux-gnueabihf 2023-09-12T10:49:09,901 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:49:09,901 Thread model: posix 2023-09-12T10:49:09,902 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:49:09,902 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:49:09,903 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/builder.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:09,904 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/builder.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase builder.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccq8ZhfF.s 2023-09-12T10:49:09,912 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:09,913 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:09,914 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:09,914 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:09,915 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:49:09,915 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:49:09,916 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:49:09,917 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:49:09,919 ignoring duplicate directory "/usr/include/" 2023-09-12T10:49:09,921 as it is a non-system directory that duplicates a system directory 2023-09-12T10:49:09,924 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:49:09,927 #include "..." search starts here: 2023-09-12T10:49:09,930 #include <...> search starts here: 2023-09-12T10:49:09,932 /usr/include/eigen3 2023-09-12T10:49:09,935 include 2023-09-12T10:49:09,938 /usr/include/python3.11 2023-09-12T10:49:09,940 /usr/include/c++/12 2023-09-12T10:49:09,942 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:49:09,945 /usr/include/c++/12/backward 2023-09-12T10:49:09,947 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:49:09,949 /usr/local/include 2023-09-12T10:49:09,951 /usr/include/arm-linux-gnueabihf 2023-09-12T10:49:09,953 /usr/include 2023-09-12T10:49:09,956 End of search list. 2023-09-12T10:49:09,958 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:09,961 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:09,966 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:09,968 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:09,971 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:49:12,438 ./src/builder.cpp:188:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:49:12,438 188 | // \ \ 2023-09-12T10:49:12,439 | ^ 2023-09-12T10:49:12,440 ./src/builder.cpp:190:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:49:12,440 190 | // \ 2023-09-12T10:49:12,441 | ^ 2023-09-12T10:49:12,442 ./src/builder.cpp:197:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:49:12,443 197 | // \ \ 2023-09-12T10:49:12,443 | ^ 2023-09-12T10:49:12,443 ./src/builder.cpp:199:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:49:12,444 199 | // \ 2023-09-12T10:49:12,444 | ^ 2023-09-12T10:49:12,445 ./src/builder.cpp:265:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:49:12,445 265 | // \ \ 2023-09-12T10:49:12,446 | ^ 2023-09-12T10:49:12,448 ./src/builder.cpp:1215:5: warning: multi-line comment [-Wcomment] 2023-09-12T10:49:12,449 1215 | // / / v2 / \ 2023-09-12T10:49:12,449 | ^ 2023-09-12T10:49:12,451 ./src/builder.cpp:1324:9: warning: multi-line comment [-Wcomment] 2023-09-12T10:49:12,451 1324 | // / \ 2023-09-12T10:49:12,452 | ^ 2023-09-12T10:49:13,651 In file included from include/openbabel/builder.h:29, 2023-09-12T10:49:13,652 from ./src/builder.cpp:22: 2023-09-12T10:49:13,652 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:49:13,653 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:49:13,654 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:49:13,654 | ^ 2023-09-12T10:49:13,655 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:49:13,655 37 | # define UNUSED(x) x 2023-09-12T10:49:13,656 | ^ 2023-09-12T10:49:14,463 In file included from include/openbabel/mol.h:52, 2023-09-12T10:49:14,463 from include/openbabel/builder.h:30: 2023-09-12T10:49:14,464 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:14,465 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:14,466 862 | {return new OBVibrationData(*this);} 2023-09-12T10:49:14,466 | ^ 2023-09-12T10:49:14,467 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:49:14,468 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:49:14,469 | ^~~~~~~~ 2023-09-12T10:49:14,469 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:14,470 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:14,471 907 | {return new OBDOSData(*this);} 2023-09-12T10:49:14,472 | ^ 2023-09-12T10:49:14,472 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:49:14,473 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:49:14,474 | ^~~~~~~~ 2023-09-12T10:49:14,488 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:14,489 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:14,490 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:49:14,491 | ^ 2023-09-12T10:49:14,491 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:49:14,492 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:49:14,492 | ^~~~~~~~ 2023-09-12T10:49:14,495 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:14,495 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:14,496 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:49:14,497 | ^ 2023-09-12T10:49:14,497 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:49:14,498 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:49:14,498 | ^~~~~~~~ 2023-09-12T10:49:14,810 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:49:14,811 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:49:14,812 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:49:14,813 | ^ 2023-09-12T10:49:14,813 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:49:14,814 37 | # define UNUSED(x) x 2023-09-12T10:49:14,815 | ^ 2023-09-12T10:49:14,815 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:49:14,816 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:49:14,817 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:49:14,818 | ^ 2023-09-12T10:49:14,818 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:49:14,819 37 | # define UNUSED(x) x 2023-09-12T10:49:14,820 | ^ 2023-09-12T10:49:14,895 In file included from include/openbabel/format.h:22, 2023-09-12T10:49:14,896 from include/openbabel/obconversion.h:37, 2023-09-12T10:49:14,897 from ./src/builder.cpp:31: 2023-09-12T10:49:14,897 include/openbabel/plugin.h: At global scope: 2023-09-12T10:49:14,898 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:49:14,899 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:49:14,899 | ^~~~~~~~~~~~~~~ 2023-09-12T10:49:14,900 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:49:14,901 from /usr/include/c++/12/vector:66, 2023-09-12T10:49:14,901 from include/openbabel/builder.h:23: 2023-09-12T10:49:14,902 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:49:14,903 131 | struct binary_function 2023-09-12T10:49:14,904 | ^~~~~~~~~~~~~~~ 2023-09-12T10:49:23,404 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:49:23,405 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::vector3&}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:49:23,405 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:49:23,406 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:49:23,406 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:49:23,847 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:49:23,847 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:49:23,848 inlined from ‘void OpenBabel::OBBuilder::LoadFragments()’ at ./src/builder.cpp:109:25: 2023-09-12T10:49:23,848 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:49:23,849 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:49:23,849 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:49:26,237 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:49:26,237 inlined from ‘static void OpenBabel::OBBuilder::ConnectFrags(OpenBabel::OBMol&, OpenBabel::OBMol&, std::vector, std::vector, std::vector)’ at ./src/builder.cpp:1243:26: 2023-09-12T10:49:26,238 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:49:26,239 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:49:26,239 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:49:27,877 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/builder.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:27,878 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/builder.o /tmp/ccq8ZhfF.s 2023-09-12T10:49:27,883 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:49:28,661 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:49:28,661 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:49:28,662 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/builder.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/builder.' 2023-09-12T10:49:28,665 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/canon.cpp -o build/temp.linux-armv7l-cpython-311/./src/canon.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:49:28,669 Using built-in specs. 2023-09-12T10:49:28,670 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:49:28,671 Target: arm-linux-gnueabihf 2023-09-12T10:49:28,671 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:49:28,672 Thread model: posix 2023-09-12T10:49:28,672 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:49:28,673 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:49:28,673 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/canon.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:28,674 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/canon.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase canon.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cczHCGDf.s 2023-09-12T10:49:28,683 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:28,684 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:28,685 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:28,685 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:28,686 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:49:28,686 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:49:28,687 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:49:28,688 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:49:28,688 ignoring duplicate directory "/usr/include/" 2023-09-12T10:49:28,689 as it is a non-system directory that duplicates a system directory 2023-09-12T10:49:28,690 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:49:28,690 #include "..." search starts here: 2023-09-12T10:49:28,691 #include <...> search starts here: 2023-09-12T10:49:28,691 /usr/include/eigen3 2023-09-12T10:49:28,691 include 2023-09-12T10:49:28,692 /usr/include/python3.11 2023-09-12T10:49:28,692 /usr/include/c++/12 2023-09-12T10:49:28,693 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:49:28,693 /usr/include/c++/12/backward 2023-09-12T10:49:28,694 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:49:28,694 /usr/local/include 2023-09-12T10:49:28,694 /usr/include/arm-linux-gnueabihf 2023-09-12T10:49:28,695 /usr/include 2023-09-12T10:49:28,695 End of search list. 2023-09-12T10:49:28,696 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:28,696 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:28,697 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:28,698 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:28,702 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:49:30,212 In file included from include/openbabel/stereo/stereo.h:27, 2023-09-12T10:49:30,213 from include/openbabel/graphsym.h:25, 2023-09-12T10:49:30,213 from ./src/canon.cpp:22: 2023-09-12T10:49:30,214 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:49:30,215 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:49:30,215 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:49:30,216 | ^ 2023-09-12T10:49:30,217 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:49:30,217 37 | # define UNUSED(x) x 2023-09-12T10:49:30,218 | ^ 2023-09-12T10:49:31,031 In file included from include/openbabel/mol.h:52, 2023-09-12T10:49:31,032 from include/openbabel/isomorphism.h:27, 2023-09-12T10:49:31,033 from include/openbabel/stereo/stereo.h:28: 2023-09-12T10:49:31,033 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:31,034 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:31,035 862 | {return new OBVibrationData(*this);} 2023-09-12T10:49:31,036 | ^ 2023-09-12T10:49:31,037 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:49:31,038 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:49:31,039 | ^~~~~~~~ 2023-09-12T10:49:31,040 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:31,041 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:31,042 907 | {return new OBDOSData(*this);} 2023-09-12T10:49:31,043 | ^ 2023-09-12T10:49:31,044 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:49:31,044 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:49:31,045 | ^~~~~~~~ 2023-09-12T10:49:31,056 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:31,057 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:31,058 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:49:31,058 | ^ 2023-09-12T10:49:31,059 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:49:31,059 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:49:31,060 | ^~~~~~~~ 2023-09-12T10:49:31,063 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:31,064 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:31,065 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:49:31,065 | ^ 2023-09-12T10:49:31,066 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:49:31,067 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:49:31,067 | ^~~~~~~~ 2023-09-12T10:49:31,509 ./src/canon.cpp: In constructor ‘OpenBabel::CanonicalLabelsImpl::State::State(const std::vector&, const OpenBabel::OBBitVec&, std::vector&, std::vector&, OpenBabel::CanonicalLabelsImpl::Orbits&, OpenBabel::OBBitVec&, bool)’: 2023-09-12T10:49:31,510 ./src/canon.cpp:708:34: warning: ‘OpenBabel::CanonicalLabelsImpl::State::stereoCenters’ will be initialized after [-Wreorder] 2023-09-12T10:49:31,510 708 | std::vector &stereoCenters; 2023-09-12T10:49:31,511 | ^~~~~~~~~~~~~ 2023-09-12T10:49:31,512 ./src/canon.cpp:702:18: warning: ‘const bool OpenBabel::CanonicalLabelsImpl::State::onlyOne’ [-Wreorder] 2023-09-12T10:49:31,513 702 | const bool onlyOne; 2023-09-12T10:49:31,513 | ^~~~~~~ 2023-09-12T10:49:31,514 ./src/canon.cpp:683:7: warning: when initialized here [-Wreorder] 2023-09-12T10:49:31,515 683 | State(const std::vector &_symmetry_classes, 2023-09-12T10:49:31,516 | ^~~~~ 2023-09-12T10:49:31,614 ./src/canon.cpp: In static member function ‘static void OpenBabel::CanonicalLabelsImpl::UpdateMcr(OpenBabel::OBBitVec&, Orbits&, OpenBabel::OBMol*, const std::vector&)’: 2023-09-12T10:49:31,705 ./src/canon.cpp:1134:65: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T10:49:31,723 1134 | static void UpdateMcr(OBBitVec &mcr, Orbits &orbits, OBMol *mol, const std::vector &bestLabels) 2023-09-12T10:49:31,774 | ~~~~~~~^~~ 2023-09-12T10:49:49,622 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/canon.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:49,623 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/canon.o /tmp/cczHCGDf.s 2023-09-12T10:49:49,629 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:49:51,022 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:49:51,023 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:49:51,023 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/canon.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/canon.' 2023-09-12T10:49:51,029 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/chains.cpp -o build/temp.linux-armv7l-cpython-311/./src/chains.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:49:51,034 Using built-in specs. 2023-09-12T10:49:51,034 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:49:51,035 Target: arm-linux-gnueabihf 2023-09-12T10:49:51,036 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:49:51,036 Thread model: posix 2023-09-12T10:49:51,037 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:49:51,037 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:49:51,038 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chains.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:49:51,039 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/chains.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase chains.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccrTH9ch.s 2023-09-12T10:49:51,048 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:51,049 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:51,049 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:51,050 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:51,050 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:49:51,051 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:49:51,051 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:49:51,052 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:49:51,052 ignoring duplicate directory "/usr/include/" 2023-09-12T10:49:51,053 as it is a non-system directory that duplicates a system directory 2023-09-12T10:49:51,054 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:49:51,055 #include "..." search starts here: 2023-09-12T10:49:51,055 #include <...> search starts here: 2023-09-12T10:49:51,056 /usr/include/eigen3 2023-09-12T10:49:51,056 include 2023-09-12T10:49:51,057 /usr/include/python3.11 2023-09-12T10:49:51,058 /usr/include/c++/12 2023-09-12T10:49:51,058 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:49:51,059 /usr/include/c++/12/backward 2023-09-12T10:49:51,060 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:49:51,061 /usr/local/include 2023-09-12T10:49:51,061 /usr/include/arm-linux-gnueabihf 2023-09-12T10:49:51,062 /usr/include 2023-09-12T10:49:51,063 End of search list. 2023-09-12T10:49:51,063 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:51,064 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:51,065 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:51,066 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:51,067 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:49:52,627 In file included from include/openbabel/atom.h:33, 2023-09-12T10:49:52,628 from include/openbabel/mol.h:43, 2023-09-12T10:49:52,628 from ./src/chains.cpp:33: 2023-09-12T10:49:52,629 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:49:52,630 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:49:52,630 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:49:52,631 | ^ 2023-09-12T10:49:52,632 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:49:52,633 37 | # define UNUSED(x) x 2023-09-12T10:49:52,633 | ^ 2023-09-12T10:49:53,389 In file included from include/openbabel/mol.h:52: 2023-09-12T10:49:53,390 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:53,391 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:53,391 862 | {return new OBVibrationData(*this);} 2023-09-12T10:49:53,392 | ^ 2023-09-12T10:49:53,392 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:49:53,393 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:49:53,393 | ^~~~~~~~ 2023-09-12T10:49:53,394 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:53,395 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:53,395 907 | {return new OBDOSData(*this);} 2023-09-12T10:49:53,396 | ^ 2023-09-12T10:49:53,397 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:49:53,397 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:49:53,398 | ^~~~~~~~ 2023-09-12T10:49:53,413 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:53,414 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:53,415 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:49:53,415 | ^ 2023-09-12T10:49:53,416 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:49:53,417 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:49:53,418 | ^~~~~~~~ 2023-09-12T10:49:53,420 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:53,421 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:53,421 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:49:53,422 | ^ 2023-09-12T10:49:53,423 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:49:53,423 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:49:53,424 | ^~~~~~~~ 2023-09-12T10:49:57,625 ./src/chains.cpp: In member function ‘void OpenBabel::OBChainsParser::ConstrainBackbone(OpenBabel::OBMol&, OpenBabel::Template*, int)’: 2023-09-12T10:49:57,625 ./src/chains.cpp:1271:51: warning: ‘nd’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:49:57,626 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:49:57,627 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:49:57,628 ./src/chains.cpp:1219:25: note: ‘nd’ was declared here 2023-09-12T10:49:57,628 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:49:57,629 | ^~ 2023-09-12T10:49:57,629 ./src/chains.cpp:1271:51: warning: ‘nc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:49:57,630 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:49:57,630 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:49:57,631 ./src/chains.cpp:1219:21: note: ‘nc’ was declared here 2023-09-12T10:49:57,631 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:49:57,632 | ^~ 2023-09-12T10:49:57,632 ./src/chains.cpp:1271:51: warning: ‘nb’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:49:57,633 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:49:57,633 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:49:57,634 ./src/chains.cpp:1219:17: note: ‘nb’ was declared here 2023-09-12T10:49:57,634 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:49:57,635 | ^~ 2023-09-12T10:49:57,635 ./src/chains.cpp:1271:51: warning: ‘na’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:49:57,636 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:49:57,636 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:49:57,637 ./src/chains.cpp:1219:13: note: ‘na’ was declared here 2023-09-12T10:49:57,638 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:49:57,638 | ^~ 2023-09-12T10:50:02,305 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chains.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:50:02,306 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/chains.o /tmp/ccrTH9ch.s 2023-09-12T10:50:02,311 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:02,869 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:50:02,870 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:50:02,870 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chains.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/chains.' 2023-09-12T10:50:02,872 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/chargemodel.cpp -o build/temp.linux-armv7l-cpython-311/./src/chargemodel.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:50:02,877 Using built-in specs. 2023-09-12T10:50:02,878 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:02,878 Target: arm-linux-gnueabihf 2023-09-12T10:50:02,879 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:50:02,879 Thread model: posix 2023-09-12T10:50:02,879 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:02,880 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:02,880 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chargemodel.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:50:02,881 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/chargemodel.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase chargemodel.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccP4Mi3t.s 2023-09-12T10:50:02,890 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:02,890 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:02,892 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:02,892 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:02,893 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:02,893 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:02,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:02,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:02,895 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:02,896 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:02,896 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:02,897 #include "..." search starts here: 2023-09-12T10:50:02,898 #include <...> search starts here: 2023-09-12T10:50:02,898 /usr/include/eigen3 2023-09-12T10:50:02,899 include 2023-09-12T10:50:02,899 /usr/include/python3.11 2023-09-12T10:50:02,900 /usr/include/c++/12 2023-09-12T10:50:02,900 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:02,900 /usr/include/c++/12/backward 2023-09-12T10:50:02,901 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:02,901 /usr/local/include 2023-09-12T10:50:02,902 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:02,902 /usr/include 2023-09-12T10:50:02,903 End of search list. 2023-09-12T10:50:02,903 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:02,903 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:02,904 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:02,905 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:02,909 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:50:04,265 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:50:04,266 from ./src/chargemodel.cpp:21: 2023-09-12T10:50:04,266 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:50:04,267 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:50:04,268 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:04,268 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:50:04,269 from include/openbabel/plugin.h:23: 2023-09-12T10:50:04,269 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:50:04,270 131 | struct binary_function 2023-09-12T10:50:04,271 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:04,414 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:50:04,415 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:50:04,416 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:50:04,417 | ~~~~~~~^ 2023-09-12T10:50:04,417 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:50:04,418 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:50:04,419 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:50:04,419 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:50:04,534 In file included from include/openbabel/atom.h:33, 2023-09-12T10:50:04,535 from include/openbabel/mol.h:43, 2023-09-12T10:50:04,535 from ./src/chargemodel.cpp:22: 2023-09-12T10:50:04,536 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:50:04,537 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:50:04,537 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:50:04,538 | ^ 2023-09-12T10:50:04,538 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:04,539 37 | # define UNUSED(x) x 2023-09-12T10:50:04,540 | ^ 2023-09-12T10:50:05,279 In file included from include/openbabel/mol.h:52: 2023-09-12T10:50:05,280 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:05,281 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:05,281 862 | {return new OBVibrationData(*this);} 2023-09-12T10:50:05,282 | ^ 2023-09-12T10:50:05,282 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:50:05,283 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:50:05,284 | ^~~~~~~~ 2023-09-12T10:50:05,285 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:05,286 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:05,286 907 | {return new OBDOSData(*this);} 2023-09-12T10:50:05,287 | ^ 2023-09-12T10:50:05,287 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:50:05,288 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:50:05,288 | ^~~~~~~~ 2023-09-12T10:50:05,304 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:05,305 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:05,306 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:50:05,306 | ^ 2023-09-12T10:50:05,307 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:50:05,308 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:50:05,309 | ^~~~~~~~ 2023-09-12T10:50:05,311 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:05,312 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:05,313 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:50:05,313 | ^ 2023-09-12T10:50:05,314 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:50:05,315 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:50:05,316 | ^~~~~~~~ 2023-09-12T10:50:06,937 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:50:06,938 from include/openbabel/plugin.h:25: 2023-09-12T10:50:06,939 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:50:06,939 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:50:06,940 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:50:06,941 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:06,982 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:50:06,983 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:50:06,984 inlined from ‘void OpenBabel::OBChargeModel::FillChargeVectors(OpenBabel::OBMol&)’ at ./src/chargemodel.cpp:44:35: 2023-09-12T10:50:06,984 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:50:06,985 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:50:06,985 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:06,986 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:50:06,986 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:50:06,987 inlined from ‘void OpenBabel::OBChargeModel::FillChargeVectors(OpenBabel::OBMol&)’ at ./src/chargemodel.cpp:45:34: 2023-09-12T10:50:06,987 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:50:06,988 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:50:06,988 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:07,063 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chargemodel.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:50:07,063 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/chargemodel.o /tmp/ccP4Mi3t.s 2023-09-12T10:50:07,068 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:07,118 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:50:07,118 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:50:07,119 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chargemodel.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/chargemodel.' 2023-09-12T10:50:07,120 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/eem.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/eem.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:50:07,124 Using built-in specs. 2023-09-12T10:50:07,125 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:07,125 Target: arm-linux-gnueabihf 2023-09-12T10:50:07,125 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:50:07,126 Thread model: posix 2023-09-12T10:50:07,126 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:07,127 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:07,127 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/eem.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:07,128 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/eem.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase eem.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccXzp83A.s 2023-09-12T10:50:07,137 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:07,137 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:07,139 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:07,139 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:07,140 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:07,140 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:07,141 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:07,141 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:07,142 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:07,143 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:07,143 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:07,144 #include "..." search starts here: 2023-09-12T10:50:07,144 #include <...> search starts here: 2023-09-12T10:50:07,145 /usr/include/eigen3 2023-09-12T10:50:07,145 include 2023-09-12T10:50:07,145 /usr/include/python3.11 2023-09-12T10:50:07,146 /usr/include/c++/12 2023-09-12T10:50:07,146 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:07,147 /usr/include/c++/12/backward 2023-09-12T10:50:07,147 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:07,148 /usr/local/include 2023-09-12T10:50:07,148 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:07,148 /usr/include 2023-09-12T10:50:07,149 End of search list. 2023-09-12T10:50:07,149 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:07,150 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:07,151 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:07,151 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:07,156 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:50:08,519 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:50:08,519 from ./src/charges/eem.cpp:23: 2023-09-12T10:50:08,520 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:50:08,521 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:50:08,521 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:08,522 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:50:08,523 from ./src/charges/eem.cpp:19: 2023-09-12T10:50:08,524 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:50:08,524 131 | struct binary_function 2023-09-12T10:50:08,525 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:08,673 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:50:08,674 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:50:08,675 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:50:08,676 | ~~~~~~~^ 2023-09-12T10:50:08,676 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:50:08,677 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:50:08,678 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:50:08,678 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:50:08,792 In file included from include/openbabel/atom.h:33, 2023-09-12T10:50:08,793 from include/openbabel/mol.h:43, 2023-09-12T10:50:08,794 from ./src/charges/eem.cpp:24: 2023-09-12T10:50:08,794 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:50:08,795 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:50:08,796 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:50:08,796 | ^ 2023-09-12T10:50:08,797 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:08,798 37 | # define UNUSED(x) x 2023-09-12T10:50:08,799 | ^ 2023-09-12T10:50:09,531 In file included from include/openbabel/mol.h:52: 2023-09-12T10:50:09,532 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:09,533 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:09,533 862 | {return new OBVibrationData(*this);} 2023-09-12T10:50:09,534 | ^ 2023-09-12T10:50:09,534 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:50:09,535 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:50:09,535 | ^~~~~~~~ 2023-09-12T10:50:09,537 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:09,538 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:09,538 907 | {return new OBDOSData(*this);} 2023-09-12T10:50:09,539 | ^ 2023-09-12T10:50:09,539 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:50:09,540 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:50:09,541 | ^~~~~~~~ 2023-09-12T10:50:09,557 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:09,557 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:09,558 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:50:09,559 | ^ 2023-09-12T10:50:09,560 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:50:09,560 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:50:09,561 | ^~~~~~~~ 2023-09-12T10:50:09,563 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:09,564 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:09,565 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:50:09,565 | ^ 2023-09-12T10:50:09,566 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:50:09,567 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:50:09,568 | ^~~~~~~~ 2023-09-12T10:50:12,417 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:50:12,418 from ./src/charges/eem.cpp:20: 2023-09-12T10:50:12,418 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::EEMParameter&}; _Tp = OpenBabel::EEMParameter; _Alloc = std::allocator]’: 2023-09-12T10:50:12,419 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:50:12,419 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:50:12,420 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:12,574 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:50:12,575 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::EEMParameter; _Alloc = std::allocator]’, 2023-09-12T10:50:12,575 inlined from ‘void OpenBabel::EEMCharges::_loadParameters()’ at ./src/charges/eem.cpp:109:28: 2023-09-12T10:50:12,576 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:50:12,576 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:50:12,577 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:50:13,935 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/eem.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:13,936 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/eem.o /tmp/ccXzp83A.s 2023-09-12T10:50:13,941 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:14,220 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:50:14,221 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:50:14,221 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/eem.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/eem.' 2023-09-12T10:50:14,223 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/eqeq.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/eqeq.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:50:14,227 Using built-in specs. 2023-09-12T10:50:14,228 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:14,229 Target: arm-linux-gnueabihf 2023-09-12T10:50:14,229 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:50:14,230 Thread model: posix 2023-09-12T10:50:14,230 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:14,231 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:14,231 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/eqeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:14,232 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/eqeq.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase eqeq.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cchGxris.s 2023-09-12T10:50:14,240 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:14,241 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:14,242 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:14,242 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:14,243 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:14,243 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:14,244 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:14,245 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:14,245 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:14,246 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:14,246 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:14,247 #include "..." search starts here: 2023-09-12T10:50:14,248 #include <...> search starts here: 2023-09-12T10:50:14,248 /usr/include/eigen3 2023-09-12T10:50:14,249 include 2023-09-12T10:50:14,250 /usr/include/python3.11 2023-09-12T10:50:14,250 /usr/include/c++/12 2023-09-12T10:50:14,251 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:14,252 /usr/include/c++/12/backward 2023-09-12T10:50:14,252 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:14,253 /usr/local/include 2023-09-12T10:50:14,254 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:14,254 /usr/include 2023-09-12T10:50:14,254 End of search list. 2023-09-12T10:50:14,255 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:14,255 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:14,256 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:14,256 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:14,258 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:50:15,858 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:50:15,859 from include/charges/eqeq.h:22, 2023-09-12T10:50:15,860 from ./src/charges/eqeq.cpp:19: 2023-09-12T10:50:15,860 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:50:15,861 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:50:15,861 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:15,862 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:50:15,862 from include/openbabel/plugin.h:23: 2023-09-12T10:50:15,863 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:50:15,863 131 | struct binary_function 2023-09-12T10:50:15,864 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:16,006 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:50:16,006 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:50:16,007 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:50:16,008 | ~~~~~~~^ 2023-09-12T10:50:16,009 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:50:16,009 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:50:16,010 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:50:16,011 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:50:16,125 In file included from include/openbabel/atom.h:33, 2023-09-12T10:50:16,126 from include/openbabel/mol.h:43, 2023-09-12T10:50:16,127 from include/charges/eqeq.h:23: 2023-09-12T10:50:16,127 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:50:16,128 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:50:16,129 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:50:16,129 | ^ 2023-09-12T10:50:16,130 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:16,130 37 | # define UNUSED(x) x 2023-09-12T10:50:16,131 | ^ 2023-09-12T10:50:16,867 In file included from include/openbabel/mol.h:52: 2023-09-12T10:50:16,868 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:16,869 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:16,869 862 | {return new OBVibrationData(*this);} 2023-09-12T10:50:16,870 | ^ 2023-09-12T10:50:16,871 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:50:16,872 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:50:16,872 | ^~~~~~~~ 2023-09-12T10:50:16,874 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:16,875 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:16,875 907 | {return new OBDOSData(*this);} 2023-09-12T10:50:16,876 | ^ 2023-09-12T10:50:16,876 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:50:16,877 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:50:16,877 | ^~~~~~~~ 2023-09-12T10:50:16,894 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:16,895 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:16,895 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:50:16,896 | ^ 2023-09-12T10:50:16,897 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:50:16,897 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:50:16,898 | ^~~~~~~~ 2023-09-12T10:50:16,902 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:16,902 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:16,903 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:50:16,904 | ^ 2023-09-12T10:50:16,905 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:50:16,905 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:50:16,906 | ^~~~~~~~ 2023-09-12T10:50:39,968 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:50:39,969 from include/openbabel/plugin.h:25: 2023-09-12T10:50:39,971 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:50:39,973 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:50:39,975 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:50:39,978 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:42,271 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:50:42,272 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:50:42,301 inlined from ‘virtual bool OpenBabel::EQEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/eqeq.cpp:187:33: 2023-09-12T10:50:42,302 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:50:42,304 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:50:42,321 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:42,322 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:50:42,323 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:50:42,324 inlined from ‘virtual bool OpenBabel::EQEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/eqeq.cpp:188:32: 2023-09-12T10:50:42,325 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:50:42,325 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:50:42,326 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:44,580 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/eqeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:44,581 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/eqeq.o /tmp/cchGxris.s 2023-09-12T10:50:44,587 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:46,619 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:50:46,620 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:50:46,620 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/eqeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/eqeq.' 2023-09-12T10:50:46,633 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/fromfile.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/fromfile.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:50:46,638 Using built-in specs. 2023-09-12T10:50:46,639 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:46,639 Target: arm-linux-gnueabihf 2023-09-12T10:50:46,640 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:50:46,640 Thread model: posix 2023-09-12T10:50:46,640 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:46,641 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:46,641 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/fromfile.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:46,642 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/fromfile.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase fromfile.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccMLQrGA.s 2023-09-12T10:50:46,652 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:46,653 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:46,654 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:46,654 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:46,655 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:46,655 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:46,656 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:46,656 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:46,657 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:46,658 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:46,658 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:46,659 #include "..." search starts here: 2023-09-12T10:50:46,660 #include <...> search starts here: 2023-09-12T10:50:46,661 /usr/include/eigen3 2023-09-12T10:50:46,661 include 2023-09-12T10:50:46,661 /usr/include/python3.11 2023-09-12T10:50:46,662 /usr/include/c++/12 2023-09-12T10:50:46,662 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:46,663 /usr/include/c++/12/backward 2023-09-12T10:50:46,663 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:46,663 /usr/local/include 2023-09-12T10:50:46,664 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:46,664 /usr/include 2023-09-12T10:50:46,665 End of search list. 2023-09-12T10:50:46,665 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:46,666 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:46,667 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:46,667 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:46,672 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:50:48,041 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:50:48,042 from ./src/charges/fromfile.cpp:21: 2023-09-12T10:50:48,042 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:50:48,043 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:50:48,043 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:48,044 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:50:48,045 from include/openbabel/plugin.h:23: 2023-09-12T10:50:48,045 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:50:48,046 131 | struct binary_function 2023-09-12T10:50:48,047 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:48,191 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:50:48,191 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:50:48,192 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:50:48,193 | ~~~~~~~^ 2023-09-12T10:50:48,193 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:50:48,194 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:50:48,195 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:50:48,196 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:50:48,309 In file included from include/openbabel/atom.h:33, 2023-09-12T10:50:48,310 from include/openbabel/mol.h:43, 2023-09-12T10:50:48,311 from ./src/charges/fromfile.cpp:22: 2023-09-12T10:50:48,311 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:50:48,312 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:50:48,313 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:50:48,313 | ^ 2023-09-12T10:50:48,314 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:48,315 37 | # define UNUSED(x) x 2023-09-12T10:50:48,316 | ^ 2023-09-12T10:50:49,049 In file included from include/openbabel/mol.h:52: 2023-09-12T10:50:49,050 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:49,051 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:49,051 862 | {return new OBVibrationData(*this);} 2023-09-12T10:50:49,052 | ^ 2023-09-12T10:50:49,052 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:50:49,053 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:50:49,053 | ^~~~~~~~ 2023-09-12T10:50:49,055 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:49,056 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:49,056 907 | {return new OBDOSData(*this);} 2023-09-12T10:50:49,057 | ^ 2023-09-12T10:50:49,058 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:50:49,058 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:50:49,059 | ^~~~~~~~ 2023-09-12T10:50:49,075 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:49,076 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:49,077 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:50:49,077 | ^ 2023-09-12T10:50:49,078 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:50:49,079 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:50:49,080 | ^~~~~~~~ 2023-09-12T10:50:49,083 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:49,084 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:49,085 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:50:49,085 | ^ 2023-09-12T10:50:49,086 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:50:49,087 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:50:49,087 | ^~~~~~~~ 2023-09-12T10:50:49,512 ./src/charges/fromfile.cpp: In member function ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:50:49,513 ./src/charges/fromfile.cpp:96:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:50:49,513 96 | for ( int i = 1; i <= mol.NumAtoms(); i++) 2023-09-12T10:50:49,514 | ~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,358 In file included from /usr/include/c++/12/map:60, 2023-09-12T10:50:52,358 from include/openbabel/plugin.h:26: 2023-09-12T10:50:52,359 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T10:50:52,360 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T10:50:52,360 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T10:50:52,361 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,980 In file included from /usr/include/c++/12/map:61: 2023-09-12T10:50:52,981 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T10:50:52,981 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:112:32: 2023-09-12T10:50:52,982 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T10:50:52,983 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:50:52,984 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,984 531 | std::forward_as_tuple(std::move(__k)), 2023-09-12T10:50:52,985 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,986 532 | std::tuple<>()); 2023-09-12T10:50:52,986 | ~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,987 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T10:50:52,988 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:120:32: 2023-09-12T10:50:52,988 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T10:50:52,989 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:50:52,990 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,991 531 | std::forward_as_tuple(std::move(__k)), 2023-09-12T10:50:52,991 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,992 532 | std::tuple<>()); 2023-09-12T10:50:52,992 | ~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,993 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T10:50:52,993 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:128:32: 2023-09-12T10:50:52,994 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T10:50:52,995 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:50:52,995 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,996 531 | std::forward_as_tuple(std::move(__k)), 2023-09-12T10:50:52,997 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:52,998 532 | std::tuple<>()); 2023-09-12T10:50:52,998 | ~~~~~~~~~~~~~~~ 2023-09-12T10:50:53,813 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/fromfile.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:53,814 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/fromfile.o /tmp/ccMLQrGA.s 2023-09-12T10:50:53,820 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:54,127 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:50:54,127 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:50:54,128 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/fromfile.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/fromfile.' 2023-09-12T10:50:54,129 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/gasteiger.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/gasteiger.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:50:54,133 Using built-in specs. 2023-09-12T10:50:54,134 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:54,135 Target: arm-linux-gnueabihf 2023-09-12T10:50:54,135 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:50:54,136 Thread model: posix 2023-09-12T10:50:54,136 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:54,137 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:54,138 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/gasteiger.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:54,138 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/gasteiger.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase gasteiger.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccBQNVLz.s 2023-09-12T10:50:54,147 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:54,148 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:54,149 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:54,149 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:54,150 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:54,150 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:54,151 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:54,151 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:54,152 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:54,152 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:54,153 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:54,153 #include "..." search starts here: 2023-09-12T10:50:54,153 #include <...> search starts here: 2023-09-12T10:50:54,154 /usr/include/eigen3 2023-09-12T10:50:54,154 include 2023-09-12T10:50:54,155 /usr/include/python3.11 2023-09-12T10:50:54,155 /usr/include/c++/12 2023-09-12T10:50:54,156 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:54,156 /usr/include/c++/12/backward 2023-09-12T10:50:54,156 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:54,157 /usr/local/include 2023-09-12T10:50:54,157 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:54,158 /usr/include 2023-09-12T10:50:54,158 End of search list. 2023-09-12T10:50:54,159 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:54,159 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:54,160 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:54,160 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:54,168 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:50:55,522 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:50:55,522 from ./src/charges/gasteiger.cpp:20: 2023-09-12T10:50:55,523 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:50:55,524 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:50:55,524 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:55,525 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:50:55,526 from include/openbabel/plugin.h:23: 2023-09-12T10:50:55,527 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:50:55,527 131 | struct binary_function 2023-09-12T10:50:55,528 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:55,671 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:50:55,671 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:50:55,672 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:50:55,673 | ~~~~~~~^ 2023-09-12T10:50:55,673 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:50:55,674 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:50:55,675 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:50:55,675 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:50:55,790 In file included from include/openbabel/atom.h:33, 2023-09-12T10:50:55,790 from include/openbabel/mol.h:43, 2023-09-12T10:50:55,791 from ./src/charges/gasteiger.cpp:21: 2023-09-12T10:50:55,792 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:50:55,793 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:50:55,793 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:50:55,794 | ^ 2023-09-12T10:50:55,794 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,795 37 | # define UNUSED(x) x 2023-09-12T10:50:55,795 | ^ 2023-09-12T10:50:56,530 In file included from include/openbabel/mol.h:52: 2023-09-12T10:50:56,531 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:56,531 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:56,532 862 | {return new OBVibrationData(*this);} 2023-09-12T10:50:56,532 | ^ 2023-09-12T10:50:56,533 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:50:56,533 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:50:56,534 | ^~~~~~~~ 2023-09-12T10:50:56,536 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:56,537 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:56,538 907 | {return new OBDOSData(*this);} 2023-09-12T10:50:56,538 | ^ 2023-09-12T10:50:56,539 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:50:56,540 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:50:56,540 | ^~~~~~~~ 2023-09-12T10:50:56,557 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:56,557 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:56,558 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:50:56,559 | ^ 2023-09-12T10:50:56,560 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:50:56,560 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:50:56,561 | ^~~~~~~~ 2023-09-12T10:50:56,564 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:56,565 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:56,566 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:50:56,566 | ^ 2023-09-12T10:50:56,567 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:50:56,568 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:50:56,569 | ^~~~~~~~ 2023-09-12T10:50:58,824 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/gasteiger.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:58,825 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/gasteiger.o /tmp/ccBQNVLz.s 2023-09-12T10:50:58,829 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:58,930 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:50:58,931 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:50:58,932 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/gasteiger.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/gasteiger.' 2023-09-12T10:50:58,933 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/mmff94.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/mmff94.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:50:58,937 Using built-in specs. 2023-09-12T10:50:58,938 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:58,939 Target: arm-linux-gnueabihf 2023-09-12T10:50:58,939 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:50:58,940 Thread model: posix 2023-09-12T10:50:58,941 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:58,941 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:58,942 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/mmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:50:58,942 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/mmff94.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase mmff94.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccbYK656.s 2023-09-12T10:50:58,951 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:58,951 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:58,953 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:58,953 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:58,954 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:58,954 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:58,955 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:58,956 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:58,956 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:58,957 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:58,958 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:58,958 #include "..." search starts here: 2023-09-12T10:50:58,959 #include <...> search starts here: 2023-09-12T10:50:58,960 /usr/include/eigen3 2023-09-12T10:50:58,960 include 2023-09-12T10:50:58,961 /usr/include/python3.11 2023-09-12T10:50:58,961 /usr/include/c++/12 2023-09-12T10:50:58,962 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:58,962 /usr/include/c++/12/backward 2023-09-12T10:50:58,963 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:58,964 /usr/local/include 2023-09-12T10:50:58,964 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:58,965 /usr/include 2023-09-12T10:50:58,965 End of search list. 2023-09-12T10:50:58,966 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:58,967 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:58,968 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:58,968 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:58,969 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:00,329 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:51:00,330 from ./src/charges/mmff94.cpp:20: 2023-09-12T10:51:00,330 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:51:00,331 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:51:00,332 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:00,333 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:51:00,333 from include/openbabel/plugin.h:23: 2023-09-12T10:51:00,334 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:51:00,334 131 | struct binary_function 2023-09-12T10:51:00,335 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:00,477 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:51:00,478 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:51:00,479 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:51:00,480 | ~~~~~~~^ 2023-09-12T10:51:00,481 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:51:00,481 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:51:00,482 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:51:00,482 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:51:00,595 In file included from include/openbabel/atom.h:33, 2023-09-12T10:51:00,596 from include/openbabel/mol.h:43, 2023-09-12T10:51:00,596 from ./src/charges/mmff94.cpp:21: 2023-09-12T10:51:00,597 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:51:00,598 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:51:00,599 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:51:00,599 | ^ 2023-09-12T10:51:00,600 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:00,601 37 | # define UNUSED(x) x 2023-09-12T10:51:00,601 | ^ 2023-09-12T10:51:01,334 In file included from include/openbabel/mol.h:52: 2023-09-12T10:51:01,335 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:01,336 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:01,337 862 | {return new OBVibrationData(*this);} 2023-09-12T10:51:01,338 | ^ 2023-09-12T10:51:01,338 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:51:01,339 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:51:01,340 | ^~~~~~~~ 2023-09-12T10:51:01,340 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:01,341 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:01,342 907 | {return new OBDOSData(*this);} 2023-09-12T10:51:01,343 | ^ 2023-09-12T10:51:01,344 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:51:01,345 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:51:01,346 | ^~~~~~~~ 2023-09-12T10:51:01,359 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:01,360 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:01,360 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:51:01,361 | ^ 2023-09-12T10:51:01,361 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:51:01,362 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:51:01,362 | ^~~~~~~~ 2023-09-12T10:51:01,365 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:01,366 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:01,366 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:51:01,367 | ^ 2023-09-12T10:51:01,368 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:51:01,368 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:51:01,369 | ^~~~~~~~ 2023-09-12T10:51:01,644 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:51:01,645 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,646 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,646 | ^ 2023-09-12T10:51:01,647 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,648 37 | # define UNUSED(x) x 2023-09-12T10:51:01,649 | ^ 2023-09-12T10:51:01,649 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:51:01,650 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,651 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,651 | ^ 2023-09-12T10:51:01,652 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,653 37 | # define UNUSED(x) x 2023-09-12T10:51:01,653 | ^ 2023-09-12T10:51:01,654 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:51:01,655 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,656 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,656 | ^ 2023-09-12T10:51:01,657 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,658 37 | # define UNUSED(x) x 2023-09-12T10:51:01,659 | ^ 2023-09-12T10:51:01,659 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:51:01,660 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,661 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,661 | ^ 2023-09-12T10:51:01,662 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,662 37 | # define UNUSED(x) x 2023-09-12T10:51:01,663 | ^ 2023-09-12T10:51:01,663 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:51:01,664 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,664 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,665 | ^ 2023-09-12T10:51:01,666 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,666 37 | # define UNUSED(x) x 2023-09-12T10:51:01,667 | ^ 2023-09-12T10:51:01,667 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:51:01,668 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,668 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,669 | ^ 2023-09-12T10:51:01,670 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,670 37 | # define UNUSED(x) x 2023-09-12T10:51:01,671 | ^ 2023-09-12T10:51:01,672 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:51:01,673 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,673 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,674 | ^ 2023-09-12T10:51:01,675 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,676 37 | # define UNUSED(x) x 2023-09-12T10:51:01,677 | ^ 2023-09-12T10:51:01,677 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:51:01,678 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:01,679 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:01,679 | ^ 2023-09-12T10:51:01,680 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:01,681 37 | # define UNUSED(x) x 2023-09-12T10:51:01,681 | ^ 2023-09-12T10:51:03,960 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:51:03,960 from include/openbabel/plugin.h:25: 2023-09-12T10:51:03,961 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:51:03,962 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:03,963 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:03,963 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,027 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:04,027 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:51:04,028 inlined from ‘virtual bool OpenBabel::MMFF94Charges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/mmff94.cpp:68:33: 2023-09-12T10:51:04,028 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:51:04,029 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:04,029 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,030 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:04,030 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:51:04,031 inlined from ‘virtual bool OpenBabel::MMFF94Charges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/mmff94.cpp:69:32: 2023-09-12T10:51:04,031 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:51:04,032 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:04,032 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,226 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/mmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:51:04,227 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/mmff94.o /tmp/ccbYK656.s 2023-09-12T10:51:04,232 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:51:04,399 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:51:04,401 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:51:04,401 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/mmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/mmff94.' 2023-09-12T10:51:04,402 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/none.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/none.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:51:04,405 Using built-in specs. 2023-09-12T10:51:04,406 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:51:04,407 Target: arm-linux-gnueabihf 2023-09-12T10:51:04,407 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:51:04,407 Thread model: posix 2023-09-12T10:51:04,408 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:51:04,409 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:51:04,409 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/none.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:51:04,409 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/none.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase none.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cctzfWqO.s 2023-09-12T10:51:04,418 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:04,419 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:04,420 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:04,421 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:04,421 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:51:04,422 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:51:04,422 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:51:04,423 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:51:04,424 ignoring duplicate directory "/usr/include/" 2023-09-12T10:51:04,424 as it is a non-system directory that duplicates a system directory 2023-09-12T10:51:04,425 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:51:04,425 #include "..." search starts here: 2023-09-12T10:51:04,426 #include <...> search starts here: 2023-09-12T10:51:04,427 /usr/include/eigen3 2023-09-12T10:51:04,427 include 2023-09-12T10:51:04,428 /usr/include/python3.11 2023-09-12T10:51:04,428 /usr/include/c++/12 2023-09-12T10:51:04,428 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:04,429 /usr/include/c++/12/backward 2023-09-12T10:51:04,429 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:04,430 /usr/local/include 2023-09-12T10:51:04,430 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:04,431 /usr/include 2023-09-12T10:51:04,431 End of search list. 2023-09-12T10:51:04,432 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:04,432 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:04,433 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:04,434 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:04,438 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:05,835 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:51:05,835 from ./src/charges/none.cpp:21: 2023-09-12T10:51:05,836 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:51:05,837 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:51:05,837 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:05,838 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:51:05,839 from include/openbabel/plugin.h:23: 2023-09-12T10:51:05,839 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:51:05,840 131 | struct binary_function 2023-09-12T10:51:05,841 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:05,984 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:51:05,985 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:51:05,985 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:51:05,986 | ~~~~~~~^ 2023-09-12T10:51:05,987 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:51:05,988 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:51:05,989 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:51:05,989 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:51:06,106 In file included from include/openbabel/atom.h:33, 2023-09-12T10:51:06,107 from include/openbabel/mol.h:43, 2023-09-12T10:51:06,107 from ./src/charges/none.cpp:22: 2023-09-12T10:51:06,108 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:51:06,109 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:51:06,109 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:51:06,110 | ^ 2023-09-12T10:51:06,111 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:06,112 37 | # define UNUSED(x) x 2023-09-12T10:51:06,112 | ^ 2023-09-12T10:51:06,851 In file included from include/openbabel/mol.h:52: 2023-09-12T10:51:06,852 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:06,853 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:06,853 862 | {return new OBVibrationData(*this);} 2023-09-12T10:51:06,854 | ^ 2023-09-12T10:51:06,854 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:51:06,855 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:51:06,856 | ^~~~~~~~ 2023-09-12T10:51:06,857 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:06,857 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:06,858 907 | {return new OBDOSData(*this);} 2023-09-12T10:51:06,859 | ^ 2023-09-12T10:51:06,859 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:51:06,860 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:51:06,860 | ^~~~~~~~ 2023-09-12T10:51:06,876 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:06,877 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:06,878 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:51:06,879 | ^ 2023-09-12T10:51:06,879 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:51:06,880 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:51:06,881 | ^~~~~~~~ 2023-09-12T10:51:06,883 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:06,884 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:06,885 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:51:06,886 | ^ 2023-09-12T10:51:06,886 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:51:06,887 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:51:06,888 | ^~~~~~~~ 2023-09-12T10:51:09,123 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/none.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:51:09,124 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/none.o /tmp/cctzfWqO.s 2023-09-12T10:51:09,129 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:51:09,237 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:51:09,237 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:51:09,238 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/none.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/none.' 2023-09-12T10:51:09,238 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/qeq.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/qeq.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:51:09,242 Using built-in specs. 2023-09-12T10:51:09,243 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:51:09,244 Target: arm-linux-gnueabihf 2023-09-12T10:51:09,244 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:51:09,245 Thread model: posix 2023-09-12T10:51:09,246 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:51:09,246 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:51:09,247 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/qeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:51:09,247 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/qeq.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase qeq.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccftvnzZ.s 2023-09-12T10:51:09,256 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:09,257 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:09,257 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:09,258 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:09,258 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:51:09,259 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:51:09,259 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:51:09,260 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:51:09,260 ignoring duplicate directory "/usr/include/" 2023-09-12T10:51:09,261 as it is a non-system directory that duplicates a system directory 2023-09-12T10:51:09,261 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:51:09,262 #include "..." search starts here: 2023-09-12T10:51:09,262 #include <...> search starts here: 2023-09-12T10:51:09,263 /usr/include/eigen3 2023-09-12T10:51:09,264 include 2023-09-12T10:51:09,264 /usr/include/python3.11 2023-09-12T10:51:09,265 /usr/include/c++/12 2023-09-12T10:51:09,266 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:09,266 /usr/include/c++/12/backward 2023-09-12T10:51:09,267 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:09,267 /usr/local/include 2023-09-12T10:51:09,268 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:09,269 /usr/include 2023-09-12T10:51:09,269 End of search list. 2023-09-12T10:51:09,270 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:09,271 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:09,272 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:09,273 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:09,277 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:10,871 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:51:10,871 from include/charges/qeq.h:22, 2023-09-12T10:51:10,872 from ./src/charges/qeq.cpp:19: 2023-09-12T10:51:10,872 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:51:10,873 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:51:10,874 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:10,874 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:51:10,875 from include/openbabel/plugin.h:23: 2023-09-12T10:51:10,876 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:51:10,877 131 | struct binary_function 2023-09-12T10:51:10,877 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:11,021 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:51:11,021 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:51:11,022 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:51:11,022 | ~~~~~~~^ 2023-09-12T10:51:11,023 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:51:11,024 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:51:11,024 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:51:11,025 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:51:11,142 In file included from include/openbabel/atom.h:33, 2023-09-12T10:51:11,142 from include/openbabel/mol.h:43, 2023-09-12T10:51:11,143 from include/charges/qeq.h:23: 2023-09-12T10:51:11,144 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:51:11,144 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:51:11,145 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:51:11,145 | ^ 2023-09-12T10:51:11,146 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:11,146 37 | # define UNUSED(x) x 2023-09-12T10:51:11,147 | ^ 2023-09-12T10:51:11,885 In file included from include/openbabel/mol.h:52: 2023-09-12T10:51:11,886 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:11,887 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:11,888 862 | {return new OBVibrationData(*this);} 2023-09-12T10:51:11,888 | ^ 2023-09-12T10:51:11,889 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:51:11,890 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:51:11,891 | ^~~~~~~~ 2023-09-12T10:51:11,893 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:11,895 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:11,895 907 | {return new OBDOSData(*this);} 2023-09-12T10:51:11,896 | ^ 2023-09-12T10:51:11,896 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:51:11,897 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:51:11,898 | ^~~~~~~~ 2023-09-12T10:51:11,915 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:11,916 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:11,917 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:51:11,918 | ^ 2023-09-12T10:51:11,918 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:51:11,919 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:51:11,919 | ^~~~~~~~ 2023-09-12T10:51:11,924 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:11,924 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:11,925 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:51:11,926 | ^ 2023-09-12T10:51:11,926 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:51:11,927 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:51:11,927 | ^~~~~~~~ 2023-09-12T10:51:14,191 ./src/charges/qeq.cpp: In member function ‘Eigen::Vector3d OpenBabel::QEqCharges::GetParameters(unsigned int, int)’: 2023-09-12T10:51:14,192 ./src/charges/qeq.cpp:148:58: warning: unused parameter ‘Q’ [-Wunused-parameter] 2023-09-12T10:51:14,193 148 | Vector3d QEqCharges::GetParameters(unsigned int Z, int Q) 2023-09-12T10:51:14,193 | ~~~~^ 2023-09-12T10:51:47,904 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:51:47,905 from include/openbabel/plugin.h:25: 2023-09-12T10:51:47,905 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Eigen::Matrix&}; _Tp = Eigen::Matrix; _Alloc = std::allocator >]’: 2023-09-12T10:51:47,906 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:51:47,907 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:47,908 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:48,044 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:51:48,045 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Eigen::Matrix; _Alloc = std::allocator >]’, 2023-09-12T10:51:48,046 inlined from ‘void OpenBabel::QEqCharges::ParseParamFile()’ at ./src/charges/qeq.cpp:143:28: 2023-09-12T10:51:48,046 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:51:48,047 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:48,048 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:48,295 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:51:48,296 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:48,297 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:48,298 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:48,449 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:51:48,449 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:52:00,021 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:52:00,022 inlined from ‘virtual bool OpenBabel::QEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qeq.cpp:280:35: 2023-09-12T10:52:00,022 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:52:00,023 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:52:00,023 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:52:00,024 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:52:00,025 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:52:00,025 inlined from ‘virtual bool OpenBabel::QEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qeq.cpp:281:34: 2023-09-12T10:52:00,026 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:52:00,026 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:00,027 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:05,264 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/qeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:52:05,269 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/qeq.o /tmp/ccftvnzZ.s 2023-09-12T10:52:05,283 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:09,185 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:52:09,186 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:52:09,187 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/qeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/qeq.' 2023-09-12T10:52:09,207 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/charges/qtpie.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/qtpie.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:52:09,211 Using built-in specs. 2023-09-12T10:52:09,212 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:09,212 Target: arm-linux-gnueabihf 2023-09-12T10:52:09,213 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:52:09,213 Thread model: posix 2023-09-12T10:52:09,214 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:09,215 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:09,215 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/qtpie.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:52:09,216 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/qtpie.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/charges/ -dumpbase qtpie.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccBVB37U.s 2023-09-12T10:52:09,225 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:09,226 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:09,227 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:09,228 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:09,229 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:09,233 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:09,234 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:09,234 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:09,235 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:09,236 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:09,236 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:09,237 #include "..." search starts here: 2023-09-12T10:52:09,238 #include <...> search starts here: 2023-09-12T10:52:09,238 /usr/include/eigen3 2023-09-12T10:52:09,239 include 2023-09-12T10:52:09,239 /usr/include/python3.11 2023-09-12T10:52:09,240 /usr/include/c++/12 2023-09-12T10:52:09,240 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:09,241 /usr/include/c++/12/backward 2023-09-12T10:52:09,241 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:09,241 /usr/local/include 2023-09-12T10:52:09,242 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:09,242 /usr/include 2023-09-12T10:52:09,243 End of search list. 2023-09-12T10:52:09,243 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:09,244 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:09,245 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:09,245 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:09,246 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:10,877 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:52:10,878 from include/charges/qtpie.h:22, 2023-09-12T10:52:10,879 from ./src/charges/qtpie.cpp:19: 2023-09-12T10:52:10,879 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:10,880 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:10,881 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:10,881 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:52:10,882 from include/openbabel/plugin.h:23: 2023-09-12T10:52:10,883 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:10,884 131 | struct binary_function 2023-09-12T10:52:10,884 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:11,025 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:52:11,026 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:52:11,027 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:52:11,027 | ~~~~~~~^ 2023-09-12T10:52:11,028 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:52:11,029 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:52:11,029 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:52:11,030 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:52:11,144 In file included from include/openbabel/atom.h:33, 2023-09-12T10:52:11,145 from include/openbabel/mol.h:43, 2023-09-12T10:52:11,146 from include/charges/qtpie.h:23: 2023-09-12T10:52:11,147 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:52:11,147 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:52:11,148 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:52:11,149 | ^ 2023-09-12T10:52:11,149 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:52:11,150 37 | # define UNUSED(x) x 2023-09-12T10:52:11,151 | ^ 2023-09-12T10:52:11,888 In file included from include/openbabel/mol.h:52: 2023-09-12T10:52:11,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:11,889 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:11,890 862 | {return new OBVibrationData(*this);} 2023-09-12T10:52:11,890 | ^ 2023-09-12T10:52:11,891 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:52:11,891 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:52:11,892 | ^~~~~~~~ 2023-09-12T10:52:11,893 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:11,894 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:11,894 907 | {return new OBDOSData(*this);} 2023-09-12T10:52:11,895 | ^ 2023-09-12T10:52:11,896 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:52:11,896 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:52:11,897 | ^~~~~~~~ 2023-09-12T10:52:11,912 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:11,913 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:11,914 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:52:11,914 | ^ 2023-09-12T10:52:11,915 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:52:11,916 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:52:11,916 | ^~~~~~~~ 2023-09-12T10:52:11,919 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:11,920 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:11,920 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:52:11,921 | ^ 2023-09-12T10:52:11,922 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:52:11,922 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:52:11,923 | ^~~~~~~~ 2023-09-12T10:52:14,195 ./src/charges/qtpie.cpp: In member function ‘Eigen::Vector3d OpenBabel::QTPIECharges::GetParameters(unsigned int, int)’: 2023-09-12T10:52:14,196 ./src/charges/qtpie.cpp:145:60: warning: unused parameter ‘Q’ [-Wunused-parameter] 2023-09-12T10:52:14,197 145 | Vector3d QTPIECharges::GetParameters(unsigned int Z, int Q) 2023-09-12T10:52:14,197 | ~~~~^ 2023-09-12T10:52:48,013 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:52:48,013 from include/openbabel/plugin.h:25: 2023-09-12T10:52:48,014 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Eigen::Matrix&}; _Tp = Eigen::Matrix; _Alloc = std::allocator >]’: 2023-09-12T10:52:48,014 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:52:48,015 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:52:48,015 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:48,152 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:52:48,153 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Eigen::Matrix; _Alloc = std::allocator >]’, 2023-09-12T10:52:48,154 inlined from ‘void OpenBabel::QTPIECharges::ParseParamFile()’ at ./src/charges/qtpie.cpp:141:28: 2023-09-12T10:52:48,154 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:52:48,155 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:52:48,156 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:52:48,405 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:52:48,405 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:52:48,406 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:52:48,407 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:48,558 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:52:48,559 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:00,254 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:00,254 inlined from ‘virtual bool OpenBabel::QTPIECharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qtpie.cpp:330:35: 2023-09-12T10:53:00,255 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:00,255 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:00,256 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:00,257 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:00,258 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:00,258 inlined from ‘virtual bool OpenBabel::QTPIECharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qtpie.cpp:331:34: 2023-09-12T10:53:00,259 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:00,260 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:00,261 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:07,192 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/qtpie.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/' 2023-09-12T10:53:07,193 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/charges/qtpie.o /tmp/ccBVB37U.s 2023-09-12T10:53:07,202 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:11,151 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:53:11,151 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:53:11,152 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/charges/qtpie.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/charges/qtpie.' 2023-09-12T10:53:11,171 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/chiral.cpp -o build/temp.linux-armv7l-cpython-311/./src/chiral.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:53:11,176 Using built-in specs. 2023-09-12T10:53:11,177 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:11,178 Target: arm-linux-gnueabihf 2023-09-12T10:53:11,179 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:53:11,179 Thread model: posix 2023-09-12T10:53:11,180 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:11,181 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:11,181 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chiral.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:53:11,182 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/chiral.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase chiral.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccC02NRJ.s 2023-09-12T10:53:11,190 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:11,191 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:11,192 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:11,192 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:11,193 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:11,193 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:11,194 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:11,195 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:11,195 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:11,196 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:11,196 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:11,197 #include "..." search starts here: 2023-09-12T10:53:11,198 #include <...> search starts here: 2023-09-12T10:53:11,198 /usr/include/eigen3 2023-09-12T10:53:11,199 include 2023-09-12T10:53:11,200 /usr/include/python3.11 2023-09-12T10:53:11,200 /usr/include/c++/12 2023-09-12T10:53:11,201 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:11,201 /usr/include/c++/12/backward 2023-09-12T10:53:11,202 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:11,203 /usr/local/include 2023-09-12T10:53:11,203 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:11,204 /usr/include 2023-09-12T10:53:11,204 End of search list. 2023-09-12T10:53:11,205 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:11,206 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:11,207 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:11,207 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:11,210 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:12,801 In file included from include/openbabel/atom.h:33, 2023-09-12T10:53:12,802 from include/openbabel/mol.h:43, 2023-09-12T10:53:12,803 from ./src/chiral.cpp:23: 2023-09-12T10:53:12,803 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:12,804 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:12,805 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:12,806 | ^ 2023-09-12T10:53:12,806 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:12,807 37 | # define UNUSED(x) x 2023-09-12T10:53:12,807 | ^ 2023-09-12T10:53:13,529 In file included from include/openbabel/mol.h:52: 2023-09-12T10:53:13,530 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:13,530 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:13,531 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:13,531 | ^ 2023-09-12T10:53:13,532 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:13,533 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:13,533 | ^~~~~~~~ 2023-09-12T10:53:13,534 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:13,535 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:13,536 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:13,536 | ^ 2023-09-12T10:53:13,537 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:13,538 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:13,538 | ^~~~~~~~ 2023-09-12T10:53:13,553 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:13,554 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:13,555 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:13,555 | ^ 2023-09-12T10:53:13,556 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:13,557 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:13,557 | ^~~~~~~~ 2023-09-12T10:53:13,560 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:13,560 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:13,561 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:13,562 | ^ 2023-09-12T10:53:13,562 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:13,563 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:13,564 | ^~~~~~~~ 2023-09-12T10:53:16,125 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:53:16,125 from include/openbabel/mol.h:35: 2023-09-12T10:53:16,126 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::vector3&}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:53:16,126 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:16,127 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:16,128 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:16,892 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:53:16,892 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:16,893 inlined from ‘double OpenBabel::CalcSignedVolume(OBMol&, OBAtom*, bool)’ at ./src/chiral.cpp:214:27: 2023-09-12T10:53:16,894 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:16,894 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:16,895 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:16,896 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:16,896 inlined from ‘double OpenBabel::CalcSignedVolume(OBMol&, OBAtom*, bool)’ at ./src/chiral.cpp:240:27: 2023-09-12T10:53:16,897 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:16,898 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:16,898 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:17,491 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chiral.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:53:17,492 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/chiral.o /tmp/ccC02NRJ.s 2023-09-12T10:53:17,496 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:17,723 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:53:17,724 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:53:17,725 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/chiral.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/chiral.' 2023-09-12T10:53:17,726 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/conformersearch.cpp -o build/temp.linux-armv7l-cpython-311/./src/conformersearch.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:53:17,730 Using built-in specs. 2023-09-12T10:53:17,731 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:17,732 Target: arm-linux-gnueabihf 2023-09-12T10:53:17,732 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:53:17,733 Thread model: posix 2023-09-12T10:53:17,734 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:17,734 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:17,735 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/conformersearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:53:17,735 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/conformersearch.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase conformersearch.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccdUOPtL.s 2023-09-12T10:53:17,743 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:17,744 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:17,745 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:17,746 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:17,747 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:17,747 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:17,748 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:17,749 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:17,749 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:17,750 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:17,750 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:17,751 #include "..." search starts here: 2023-09-12T10:53:17,751 #include <...> search starts here: 2023-09-12T10:53:17,751 /usr/include/eigen3 2023-09-12T10:53:17,752 include 2023-09-12T10:53:17,752 /usr/include/python3.11 2023-09-12T10:53:17,753 /usr/include/c++/12 2023-09-12T10:53:17,753 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:17,754 /usr/include/c++/12/backward 2023-09-12T10:53:17,754 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:17,755 /usr/local/include 2023-09-12T10:53:17,755 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:17,756 /usr/include 2023-09-12T10:53:17,756 End of search list. 2023-09-12T10:53:17,756 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:17,757 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:17,758 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:17,758 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:17,765 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:19,540 In file included from include/openbabel/atom.h:33, 2023-09-12T10:53:19,540 from include/openbabel/mol.h:43, 2023-09-12T10:53:19,541 from include/openbabel/conformersearch.h:24, 2023-09-12T10:53:19,542 from ./src/conformersearch.cpp:20: 2023-09-12T10:53:19,544 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:19,544 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:19,545 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:19,546 | ^ 2023-09-12T10:53:19,547 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:19,551 37 | # define UNUSED(x) x 2023-09-12T10:53:19,552 | ^ 2023-09-12T10:53:20,312 In file included from include/openbabel/mol.h:52: 2023-09-12T10:53:20,313 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:20,313 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:20,314 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:20,315 | ^ 2023-09-12T10:53:20,316 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:20,316 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:20,317 | ^~~~~~~~ 2023-09-12T10:53:20,318 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:20,319 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:20,320 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:20,321 | ^ 2023-09-12T10:53:20,322 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:20,322 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:20,323 | ^~~~~~~~ 2023-09-12T10:53:20,337 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:20,337 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:20,338 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:20,339 | ^ 2023-09-12T10:53:20,339 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:20,340 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:20,340 | ^~~~~~~~ 2023-09-12T10:53:20,343 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:20,344 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:20,347 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:20,348 | ^ 2023-09-12T10:53:20,349 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:20,357 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:20,358 | ^~~~~~~~ 2023-09-12T10:53:20,553 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:53:20,554 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:53:20,554 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:53:20,555 | ^ 2023-09-12T10:53:20,556 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:20,556 37 | # define UNUSED(x) x 2023-09-12T10:53:20,557 | ^ 2023-09-12T10:53:20,558 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:53:20,559 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:53:20,559 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:53:20,560 | ^ 2023-09-12T10:53:20,561 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:20,561 37 | # define UNUSED(x) x 2023-09-12T10:53:20,562 | ^ 2023-09-12T10:53:22,311 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:53:22,311 from ./src/conformersearch.cpp:22: 2023-09-12T10:53:22,312 include/openbabel/plugin.h: At global scope: 2023-09-12T10:53:22,313 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:53:22,314 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:53:22,315 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:22,315 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:53:22,316 from /usr/include/c++/12/vector:66, 2023-09-12T10:53:22,316 from include/openbabel/mol.h:35: 2023-09-12T10:53:22,317 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:53:22,317 131 | struct binary_function 2023-09-12T10:53:22,318 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:22,453 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:53:22,454 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,455 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,455 | ^ 2023-09-12T10:53:22,456 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,461 37 | # define UNUSED(x) x 2023-09-12T10:53:22,462 | ^ 2023-09-12T10:53:22,462 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:53:22,463 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,463 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,464 | ^ 2023-09-12T10:53:22,465 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,465 37 | # define UNUSED(x) x 2023-09-12T10:53:22,466 | ^ 2023-09-12T10:53:22,467 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:53:22,467 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,468 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,469 | ^ 2023-09-12T10:53:22,469 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,470 37 | # define UNUSED(x) x 2023-09-12T10:53:22,471 | ^ 2023-09-12T10:53:22,471 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:53:22,472 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,473 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,474 | ^ 2023-09-12T10:53:22,474 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,475 37 | # define UNUSED(x) x 2023-09-12T10:53:22,476 | ^ 2023-09-12T10:53:22,476 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:53:22,477 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,478 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,478 | ^ 2023-09-12T10:53:22,479 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,480 37 | # define UNUSED(x) x 2023-09-12T10:53:22,481 | ^ 2023-09-12T10:53:22,481 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:53:22,482 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,483 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,484 | ^ 2023-09-12T10:53:22,484 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,485 37 | # define UNUSED(x) x 2023-09-12T10:53:22,485 | ^ 2023-09-12T10:53:22,486 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:53:22,487 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,487 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,488 | ^ 2023-09-12T10:53:22,488 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,489 37 | # define UNUSED(x) x 2023-09-12T10:53:22,489 | ^ 2023-09-12T10:53:22,490 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:53:22,491 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:22,491 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:22,492 | ^ 2023-09-12T10:53:22,492 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:22,493 37 | # define UNUSED(x) x 2023-09-12T10:53:22,494 | ^ 2023-09-12T10:53:22,494 ./src/conformersearch.cpp: In member function ‘virtual bool OpenBabel::OBStericConformerFilter::IsGood(const OpenBabel::OBMol&, const OpenBabel::RotorKey&, double*)’: 2023-09-12T10:53:22,495 ./src/conformersearch.cpp:48:74: warning: unused parameter ‘key’ [-Wunused-parameter] 2023-09-12T10:53:22,496 48 | bool OBStericConformerFilter::IsGood(const OBMol &mol, const RotorKey &key, double *conformer) 2023-09-12T10:53:22,497 | ~~~~~~~~~~~~~~~~^~~ 2023-09-12T10:53:22,497 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2023-09-12T10:53:22,498 ./src/conformersearch.cpp:97:55: warning: unused parameter ‘keys’ [-Wunused-parameter] 2023-09-12T10:53:22,499 97 | const RotorKeys &keys, const std::vector &conformers) 2023-09-12T10:53:22,500 | ~~~~~~~~~~~~~~~~~^~~~ 2023-09-12T10:53:22,512 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2023-09-12T10:53:22,513 ./src/conformersearch.cpp:240:12: warning: unused variable ‘score’ [-Wunused-variable] 2023-09-12T10:53:22,514 240 | double score = ff->Energy(false); // no gradients 2023-09-12T10:53:22,514 | ^~~~~ 2023-09-12T10:53:22,515 ./src/conformersearch.cpp:221:65: warning: unused parameter ‘keys’ [-Wunused-parameter] 2023-09-12T10:53:22,516 221 | const RotorKeys &keys, const std::vector &conformers) 2023-09-12T10:53:22,517 | ~~~~~~~~~~~~~~~~~^~~~ 2023-09-12T10:53:22,524 ./src/conformersearch.cpp: In member function ‘bool OpenBabel::OBConformerSearch::Setup(const OpenBabel::OBMol&, int, int, int, int)’: 2023-09-12T10:53:22,525 ./src/conformersearch.cpp:337:23: warning: variable ‘end_it’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:53:22,526 337 | OBRotorIterator end_it = m_rotorList.EndRotors(); 2023-09-12T10:53:22,527 | ^~~~~~ 2023-09-12T10:53:22,593 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::local_opt()’: 2023-09-12T10:53:22,594 ./src/conformersearch.cpp:775:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:22,594 775 | for (i = 1; i <= m_rotorList.Size(); ++i, rotor = m_rotorList.NextRotor(ri)) 2023-09-12T10:53:22,595 | ~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:22,599 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::reproduce(OpenBabel::RotorKey&, OpenBabel::RotorKey&)’: 2023-09-12T10:53:22,600 ./src/conformersearch.cpp:836:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:22,600 836 | if (iniche > -1) 2023-09-12T10:53:22,601 | ~~~~~~~^~~~ 2023-09-12T10:53:22,615 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::share_fitness()’: 2023-09-12T10:53:22,615 ./src/conformersearch.cpp:991:37: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T10:53:22,616 991 | if ((dynamic_niches.size () < nb_niches) && (dynamic_niches.size () %2)) 2023-09-12T10:53:22,616 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T10:53:22,617 ./src/conformersearch.cpp:1006:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:53:22,618 1006 | if (dist < min_dist ) 2023-09-12T10:53:22,618 | ~~~~~^~~~~~~~~~ 2023-09-12T10:53:22,619 ./src/conformersearch.cpp:1019:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:22,620 1019 | if (imax == -1) 2023-09-12T10:53:22,621 | ~~~~~^~~~~ 2023-09-12T10:53:22,622 ./src/conformersearch.cpp:1035:40: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T10:53:22,622 1035 | if (dynamic_niches.size () < nb_niches) 2023-09-12T10:53:22,623 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T10:53:22,624 ./src/conformersearch.cpp:962:10: warning: unused variable ‘flag_niched’ [-Wunused-variable] 2023-09-12T10:53:22,625 962 | bool flag_niched = false; 2023-09-12T10:53:22,625 | ^~~~~~~~~~~ 2023-09-12T10:53:22,632 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::sharing_generation()’: 2023-09-12T10:53:22,633 ./src/conformersearch.cpp:1124:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:53:22,634 1124 | while (ninsert < ((half_pop * 2) / 3)) 2023-09-12T10:53:22,634 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:22,635 ./src/conformersearch.cpp:1133:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:53:22,636 1133 | if (iround < imax) 2023-09-12T10:53:22,636 | ~~~~~~~^~~~~~ 2023-09-12T10:53:22,637 ./src/conformersearch.cpp:1141:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:53:22,638 1141 | if (ninsert >= half_pop) 2023-09-12T10:53:22,639 | ~~~~~~~~^~~~~~~~~~~ 2023-09-12T10:53:22,640 ./src/conformersearch.cpp:1166:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:53:22,640 1166 | while (ninsert < half_pop) 2023-09-12T10:53:22,641 | ~~~~~~~~^~~~~~~~~~ 2023-09-12T10:53:22,641 ./src/conformersearch.cpp:1090:23: warning: unused variable ‘lowest’ [-Wunused-variable] 2023-09-12T10:53:22,642 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2023-09-12T10:53:22,642 | ^~~~~~ 2023-09-12T10:53:22,643 ./src/conformersearch.cpp:1090:37: warning: unused variable ‘highest’ [-Wunused-variable] 2023-09-12T10:53:22,643 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2023-09-12T10:53:22,644 | ^~~~~~~ 2023-09-12T10:53:26,729 In file included from /usr/include/c++/12/algorithm:61, 2023-09-12T10:53:26,730 from include/openbabel/ring.h:24, 2023-09-12T10:53:26,730 from include/openbabel/mol.h:51: 2023-09-12T10:53:26,731 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: 2023-09-12T10:53:26,731 /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:26,732 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, 2023-09-12T10:53:26,732 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:26,798 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: 2023-09-12T10:53:26,799 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:26,800 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:53:26,800 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:53:26,801 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:26,859 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: 2023-09-12T10:53:26,860 /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:26,860 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, 2023-09-12T10:53:26,861 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:26,926 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: 2023-09-12T10:53:26,927 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:26,928 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:53:26,928 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:53:26,929 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:27,008 In file included from /usr/include/c++/12/bits/stl_algo.h:60: 2023-09-12T10:53:27,009 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OpenBabel::ConformerScore; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: 2023-09-12T10:53:27,009 /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:27,010 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T10:53:27,011 | ^~~~~~~~~~~~~ 2023-09-12T10:53:27,277 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OpenBabel::ConformerScore; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: 2023-09-12T10:53:27,277 /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:28,340 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:53:28,341 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:53:28,341 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:28,342 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:28,343 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:28,741 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:53:28,741 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:28,890 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:28,890 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:28,891 inlined from ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:249:19: 2023-09-12T10:53:28,892 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:28,893 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:28,894 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:28,894 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:28,895 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:28,896 inlined from ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:262:21: 2023-09-12T10:53:28,896 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:28,897 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:28,897 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,119 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:29,120 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:29,121 inlined from ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:105:19: 2023-09-12T10:53:29,121 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,122 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:29,123 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,124 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:29,124 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:29,125 inlined from ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:118:21: 2023-09-12T10:53:29,126 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,127 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:29,127 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,254 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::ConformerScore}; _Tp = OpenBabel::ConformerScore; _Alloc = std::allocator]’: 2023-09-12T10:53:29,255 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:29,256 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:29,257 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,423 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: 2023-09-12T10:53:29,424 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,425 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:53:29,425 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,426 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,427 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,427 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:53:29,428 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,705 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: 2023-09-12T10:53:29,706 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,706 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:53:29,707 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,708 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,709 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:29,710 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:53:29,710 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:29,884 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:53:29,885 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:29,885 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:29,886 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,046 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:30,046 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:30,047 inlined from ‘int OpenBabel::OBConformerSearch::share_fitness()’ at ./src/conformersearch.cpp:979:34: 2023-09-12T10:53:30,048 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,048 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:30,049 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,050 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:30,050 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:30,051 inlined from ‘int OpenBabel::OBConformerSearch::share_fitness()’ at ./src/conformersearch.cpp:982:34: 2023-09-12T10:53:30,052 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,052 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:30,053 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,726 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::ConformerScore}; _Tp = OpenBabel::ConformerScore; _Alloc = std::allocator]’, 2023-09-12T10:53:30,726 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::ConformerScore; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:30,727 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:927:35: 2023-09-12T10:53:30,727 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,728 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:30,729 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,729 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:30,730 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:30,731 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2023-09-12T10:53:30,732 /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,732 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:53:30,733 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,734 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:53:30,735 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,735 1939 | __comp); 2023-09-12T10:53:30,736 | ~~~~~~~ 2023-09-12T10:53:30,737 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:30,737 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-12T10:53:30,738 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:30,739 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2023-09-12T10:53:30,739 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,740 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:53:30,741 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,741 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,742 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:53:30,742 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,743 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:30,744 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:30,745 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2023-09-12T10:53:30,746 /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,746 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:53:30,747 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,748 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:53:30,748 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,749 1939 | __comp); 2023-09-12T10:53:30,749 | ~~~~~~~ 2023-09-12T10:53:30,750 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:30,751 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-12T10:53:30,751 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:30,752 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2023-09-12T10:53:30,753 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,754 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:53:30,754 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,755 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,755 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:53:30,756 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:30,756 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:53:30,757 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:30,758 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:946:27: 2023-09-12T10:53:30,758 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:30,759 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:30,760 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:31,190 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::MakeSelection()’: 2023-09-12T10:53:31,191 ./src/conformersearch.cpp:535:31: warning: ‘highest’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:31,192 535 | double sum = 0.0, lowest, highest; 2023-09-12T10:53:31,192 | ^~~~~~~ 2023-09-12T10:53:31,202 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::ConformerScore}; _Tp = OpenBabel::ConformerScore; _Alloc = std::allocator]’, 2023-09-12T10:53:31,203 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::ConformerScore; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:31,204 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:516:33: 2023-09-12T10:53:31,205 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:31,206 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:31,206 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,207 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:31,208 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:31,208 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2023-09-12T10:53:31,209 /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:31,210 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:53:31,211 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,212 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:53:31,212 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,213 1939 | __comp); 2023-09-12T10:53:31,213 | ~~~~~~~ 2023-09-12T10:53:31,214 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:31,214 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-12T10:53:31,215 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:31,216 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2023-09-12T10:53:31,216 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:31,217 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:53:31,218 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,218 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:31,219 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:53:31,220 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,221 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:31,222 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:31,222 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2023-09-12T10:53:31,223 /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:31,224 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:53:31,224 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,225 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:53:31,226 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,227 1939 | __comp); 2023-09-12T10:53:31,227 | ~~~~~~~ 2023-09-12T10:53:31,228 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:53:31,228 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-12T10:53:31,229 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:31,229 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2023-09-12T10:53:31,230 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:31,230 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:53:31,231 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:31,232 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:31,232 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:53:31,233 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,022 In file included from /usr/include/c++/12/map:60, 2023-09-12T10:53:33,023 from include/openbabel/mol.h:37: 2023-09-12T10:53:33,023 /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::vector; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T10:53:33,024 /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T10:53:33,025 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T10:53:33,026 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:35,593 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/conformersearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:53:35,594 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/conformersearch.o /tmp/ccdUOPtL.s 2023-09-12T10:53:35,599 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:36,702 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:53:36,702 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:53:36,703 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/conformersearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/conformersearch.' 2023-09-12T10:53:36,708 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/confsearch.cpp -o build/temp.linux-armv7l-cpython-311/./src/confsearch.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:53:36,712 Using built-in specs. 2023-09-12T10:53:36,713 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:36,714 Target: arm-linux-gnueabihf 2023-09-12T10:53:36,714 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:53:36,715 Thread model: posix 2023-09-12T10:53:36,715 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:36,716 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:36,716 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/confsearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:53:36,717 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/confsearch.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase confsearch.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccyRf2iW.s 2023-09-12T10:53:36,726 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:36,726 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:36,727 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:36,728 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:36,728 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:36,729 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:36,729 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:36,730 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:36,730 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:36,731 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:36,731 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:36,731 #include "..." search starts here: 2023-09-12T10:53:36,732 #include <...> search starts here: 2023-09-12T10:53:36,732 /usr/include/eigen3 2023-09-12T10:53:36,733 include 2023-09-12T10:53:36,733 /usr/include/python3.11 2023-09-12T10:53:36,734 /usr/include/c++/12 2023-09-12T10:53:36,734 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:36,735 /usr/include/c++/12/backward 2023-09-12T10:53:36,736 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:36,736 /usr/local/include 2023-09-12T10:53:36,737 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:36,738 /usr/include 2023-09-12T10:53:36,738 End of search list. 2023-09-12T10:53:36,739 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:36,739 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:36,740 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:36,741 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:36,744 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:38,517 In file included from include/openbabel/forcefield.h:30, 2023-09-12T10:53:38,518 from ./src/confsearch.cpp:23: 2023-09-12T10:53:38,519 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:38,519 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:38,520 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:38,521 | ^ 2023-09-12T10:53:38,521 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:38,522 37 | # define UNUSED(x) x 2023-09-12T10:53:38,522 | ^ 2023-09-12T10:53:39,326 In file included from include/openbabel/mol.h:52, 2023-09-12T10:53:39,326 from include/openbabel/forcefield.h:31: 2023-09-12T10:53:39,327 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:39,328 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:39,329 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:39,330 | ^ 2023-09-12T10:53:39,330 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:39,331 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:39,332 | ^~~~~~~~ 2023-09-12T10:53:39,332 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:39,333 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:39,333 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:39,334 | ^ 2023-09-12T10:53:39,335 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:39,335 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:39,336 | ^~~~~~~~ 2023-09-12T10:53:39,350 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:39,351 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:39,351 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:39,352 | ^ 2023-09-12T10:53:39,353 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:39,354 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:39,355 | ^~~~~~~~ 2023-09-12T10:53:39,357 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:39,358 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:39,358 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:39,359 | ^ 2023-09-12T10:53:39,360 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:39,361 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:39,361 | ^~~~~~~~ 2023-09-12T10:53:39,532 In file included from include/openbabel/forcefield.h:32: 2023-09-12T10:53:39,532 include/openbabel/plugin.h: At global scope: 2023-09-12T10:53:39,533 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:53:39,534 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:53:39,535 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:39,536 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:53:39,536 from /usr/include/c++/12/vector:66, 2023-09-12T10:53:39,537 from include/openbabel/forcefield.h:23: 2023-09-12T10:53:39,538 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:53:39,538 131 | struct binary_function 2023-09-12T10:53:39,539 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:39,659 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:53:39,659 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,660 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,661 | ^ 2023-09-12T10:53:39,661 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,662 37 | # define UNUSED(x) x 2023-09-12T10:53:39,662 | ^ 2023-09-12T10:53:39,663 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:53:39,664 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,664 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,665 | ^ 2023-09-12T10:53:39,666 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,666 37 | # define UNUSED(x) x 2023-09-12T10:53:39,667 | ^ 2023-09-12T10:53:39,667 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:53:39,668 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,669 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,670 | ^ 2023-09-12T10:53:39,671 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,672 37 | # define UNUSED(x) x 2023-09-12T10:53:39,672 | ^ 2023-09-12T10:53:39,673 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:53:39,674 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,675 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,675 | ^ 2023-09-12T10:53:39,676 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,677 37 | # define UNUSED(x) x 2023-09-12T10:53:39,678 | ^ 2023-09-12T10:53:39,678 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:53:39,679 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,680 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,680 | ^ 2023-09-12T10:53:39,681 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,682 37 | # define UNUSED(x) x 2023-09-12T10:53:39,682 | ^ 2023-09-12T10:53:39,683 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:53:39,684 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,685 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,685 | ^ 2023-09-12T10:53:39,686 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,687 37 | # define UNUSED(x) x 2023-09-12T10:53:39,687 | ^ 2023-09-12T10:53:39,688 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:53:39,688 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,689 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,690 | ^ 2023-09-12T10:53:39,690 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,691 37 | # define UNUSED(x) x 2023-09-12T10:53:39,691 | ^ 2023-09-12T10:53:39,692 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:53:39,692 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:39,693 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:39,694 | ^ 2023-09-12T10:53:39,695 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,695 37 | # define UNUSED(x) x 2023-09-12T10:53:39,696 | ^ 2023-09-12T10:53:39,709 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:53:39,710 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:53:39,710 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:53:39,711 | ^ 2023-09-12T10:53:39,712 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,713 37 | # define UNUSED(x) x 2023-09-12T10:53:39,713 | ^ 2023-09-12T10:53:39,714 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:53:39,715 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:53:39,716 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:53:39,716 | ^ 2023-09-12T10:53:39,717 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:39,718 37 | # define UNUSED(x) x 2023-09-12T10:53:39,719 | ^ 2023-09-12T10:53:41,795 ./src/confsearch.cpp: In member function ‘unsigned int OpenBabel::LFSR::GetNext()’: 2023-09-12T10:53:41,795 ./src/confsearch.cpp:86:47: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 2023-09-12T10:53:41,796 86 | _lfsr = (_lfsr >> 1) ^ (unsigned int)(0 - (_lfsr & 1u) & _poly); 2023-09-12T10:53:41,797 | ~~^~~~~~~~~~~~~~ 2023-09-12T10:53:41,807 ./src/confsearch.cpp: In constructor ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’: 2023-09-12T10:53:41,807 ./src/confsearch.cpp:125:20: warning: ‘OpenBabel::OBDiversePoses::cutoff’ will be initialized after [-Wreorder] 2023-09-12T10:53:41,808 125 | const double cutoff; 2023-09-12T10:53:41,809 | ^~~~~~ 2023-09-12T10:53:41,810 ./src/confsearch.cpp:119:12: warning: ‘bool OpenBabel::OBDiversePoses::_percise’ [-Wreorder] 2023-09-12T10:53:41,810 119 | bool _percise; 2023-09-12T10:53:41,811 | ^~~~~~~~ 2023-09-12T10:53:41,812 ./src/confsearch.cpp:139:3: warning: when initialized here [-Wreorder] 2023-09-12T10:53:41,813 139 | OBDiversePoses::OBDiversePoses(const OBMol &ref, double RMSD, bool percise): 2023-09-12T10:53:41,814 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:41,815 ./src/confsearch.cpp:149:66: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T10:53:41,815 149 | vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less(), (cutoff + 0.1) )), vec.end()); 2023-09-12T10:53:41,816 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:41,816 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T10:53:41,817 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T10:53:41,817 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T10:53:41,818 | ^~~~~~~ 2023-09-12T10:53:41,824 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(double*, double, int)’: 2023-09-12T10:53:41,825 ./src/confsearch.cpp:166:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:41,825 166 | for (unsigned int a = 0; a < natoms; ++a) 2023-09-12T10:53:41,826 | ~~^~~~~~~~ 2023-09-12T10:53:41,861 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’: 2023-09-12T10:53:41,862 ./src/confsearch.cpp:205:14: warning: unused variable ‘min_rmsd’ [-Wunused-variable] 2023-09-12T10:53:41,863 205 | double min_rmsd = DBL_MAX; 2023-09-12T10:53:41,863 | ^~~~~~~~ 2023-09-12T10:53:41,866 ./src/confsearch.cpp:269:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:41,867 269 | for (int k = *c; k < levels.size(); ++k) { 2023-09-12T10:53:41,867 | ~~^~~~~~~~~~~~~~~ 2023-09-12T10:53:41,868 ./src/confsearch.cpp: In member function ‘std::vector OpenBabel::OBDiversePoses::GetHeavyAtomCoords(const std::vector&)’: 2023-09-12T10:53:41,869 ./src/confsearch.cpp:283:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:41,870 283 | for (unsigned int a = 0; a < natoms; ++a) 2023-09-12T10:53:41,871 | ~~^~~~~~~~ 2023-09-12T10:53:41,889 ./src/confsearch.cpp: In member function ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’: 2023-09-12T10:53:41,890 ./src/confsearch.cpp:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:41,891 426 | for (int i = 1; i < rl.Size() + 1; ++i, rotor = rl.NextRotor(ri)) { // foreach rotor 2023-09-12T10:53:41,892 | ~~^~~~~~~~~~~~~~~ 2023-09-12T10:53:41,902 ./src/confsearch.cpp:464:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:41,903 464 | for (int i = 0 ; i < rotor_sizes.size(); ++i) { 2023-09-12T10:53:41,903 | ~~^~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:41,904 ./src/confsearch.cpp:479:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:53:41,905 479 | } while (combination != 1 && counter < nconfs); // The LFSR always terminates with a 1 2023-09-12T10:53:41,906 | ~~~~~~~~^~~~~~~~ 2023-09-12T10:53:41,908 ./src/confsearch.cpp:489:77: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = plus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T10:53:41,909 489 | transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(plus(), energy_offset)); 2023-09-12T10:53:41,910 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:41,910 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T10:53:41,911 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T10:53:41,911 | ^~~~~~~ 2023-09-12T10:53:41,912 ./src/confsearch.cpp:402:9: warning: unused variable ‘origLogLevel’ [-Wunused-variable] 2023-09-12T10:53:41,912 402 | int origLogLevel = _loglvl; 2023-09-12T10:53:41,913 | ^~~~~~~~~~~~ 2023-09-12T10:53:47,610 In file included from /usr/include/c++/12/vector:60: 2023-09-12T10:53:47,610 /usr/include/c++/12/bits/stl_algobase.h: In function ‘_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred > >]’: 2023-09-12T10:53:47,611 /usr/include/c++/12/bits/stl_algobase.h:2131:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:47,611 2131 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, 2023-09-12T10:53:47,612 | ^~~~~~~~~~~ 2023-09-12T10:53:47,612 /usr/include/c++/12/bits/stl_algobase.h:2131:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:47,655 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:53:47,656 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:53:47,657 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:47,657 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:47,658 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:47,785 In file included from /usr/include/c++/12/algorithm:61, 2023-09-12T10:53:47,786 from include/openbabel/ring.h:24, 2023-09-12T10:53:47,786 from include/openbabel/mol.h:51: 2023-09-12T10:53:47,787 In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator >; _Predicate = binder2nd >]’, 2023-09-12T10:53:47,788 inlined from ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’ at ./src/confsearch.cpp:149:29: 2023-09-12T10:53:47,789 /usr/include/c++/12/bits/stl_algo.h:877:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:47,789 877 | return std::__remove_if(__first, __last, 2023-09-12T10:53:47,790 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:53:47,791 878 | __gnu_cxx::__ops::__pred_iter(__pred)); 2023-09-12T10:53:47,792 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:47,793 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:53:47,793 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:47,794 inlined from ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’ at ./src/confsearch.cpp:150:18: 2023-09-12T10:53:47,795 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:47,796 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:47,809 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:48,050 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::vector3&}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:53:48,050 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:48,051 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:48,051 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:48,105 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:48,106 inlined from ‘std::vector OpenBabel::GetHeavyAtomCoords(const OBMol*, const std::vector&)’ at ./src/confsearch.cpp:302:27: 2023-09-12T10:53:48,107 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:48,107 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:48,108 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:48,142 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:48,143 inlined from ‘std::vector OpenBabel::OBDiversePoses::GetHeavyAtomCoords(const std::vector&)’ at ./src/confsearch.cpp:285:29: 2023-09-12T10:53:48,143 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:48,144 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:48,145 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:48,218 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::triple >, double, int>&}; _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’: 2023-09-12T10:53:48,219 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector, double, int> >::iterator’ changed in GCC 7.1 2023-09-12T10:53:48,220 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:48,220 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:48,521 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:53:48,522 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:48,651 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::triple >, double, int>}; _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’: 2023-09-12T10:53:48,652 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector, double, int> >::iterator’ changed in GCC 7.1 2023-09-12T10:53:48,948 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:48,949 inlined from ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’ at ./src/confsearch.cpp:225:36: 2023-09-12T10:53:48,949 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:48,950 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:48,950 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:48,951 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::triple >, double, int>}; _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’, 2023-09-12T10:53:48,952 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:48,952 inlined from ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’ at ./src/confsearch.cpp:240:30: 2023-09-12T10:53:48,953 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:48,954 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:48,954 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,386 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:49,386 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:49,387 inlined from ‘bool OpenBabel::OBDiversePoses::AddPose(double*, double, int)’ at ./src/confsearch.cpp:167:24: 2023-09-12T10:53:49,388 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:49,389 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:49,389 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,472 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:53:49,473 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:49,474 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:49,474 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,642 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’: 2023-09-12T10:53:49,643 /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:49,644 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, 2023-09-12T10:53:49,644 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,718 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’: 2023-09-12T10:53:49,718 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:49,719 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:53:49,719 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,720 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:49,805 In file included from /usr/include/c++/12/bits/stl_algo.h:60: 2023-09-12T10:53:49,805 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Distance = int; _Tp = OpenBabel::triple, double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’: 2023-09-12T10:53:49,806 /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:49,807 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T10:53:49,808 | ^~~~~~~~~~~~~ 2023-09-12T10:53:49,917 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’: 2023-09-12T10:53:49,918 /usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:49,918 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, 2023-09-12T10:53:49,919 | ^~~~~~~~~~~ 2023-09-12T10:53:49,920 /usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,057 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’: 2023-09-12T10:53:50,058 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,059 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:53:50,059 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,060 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,061 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,062 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:53:50,062 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,063 In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’, 2023-09-12T10:53:50,064 inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25, 2023-09-12T10:53:50,065 inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27: 2023-09-12T10:53:50,066 /usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,066 1629 | std::__make_heap(__first, __middle, __comp); 2023-09-12T10:53:50,067 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,412 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’, 2023-09-12T10:53:50,413 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:318:22: 2023-09-12T10:53:50,414 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,414 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:50,415 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:50,416 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’, 2023-09-12T10:53:50,416 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = bool (*)(const OpenBabel::triple, double, int>&, const OpenBabel::triple, double, int>&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:50,417 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2023-09-12T10:53:50,418 /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,419 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:53:50,419 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,420 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:53:50,421 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,421 1939 | __comp); 2023-09-12T10:53:50,422 | ~~~~~~~ 2023-09-12T10:53:50,423 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’, 2023-09-12T10:53:50,424 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, double, int>&, const OpenBabel::triple, double, int>&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-12T10:53:50,424 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator, double, int>*, vector, double, int> > >; _Compare = bool (*)(const OpenBabel::triple, double, int>&, const OpenBabel::triple, double, int>&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:53:50,425 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2023-09-12T10:53:50,426 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,427 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:53:50,427 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,428 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,428 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:53:50,429 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,430 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’, 2023-09-12T10:53:50,430 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:334:25: 2023-09-12T10:53:50,431 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2023-09-12T10:53:50,432 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:50,433 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:50,434 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:50,434 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:363:25: 2023-09-12T10:53:50,435 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:50,436 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:50,436 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:51,009 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:51,010 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:53:51,010 inlined from ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’ at ./src/confsearch.cpp:393:26: 2023-09-12T10:53:51,011 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:51,012 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:51,012 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:51,013 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:51,014 inlined from ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’ at ./src/confsearch.cpp:420:24: 2023-09-12T10:53:51,014 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:51,015 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:51,015 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:52,992 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:52,993 inlined from ‘int OpenBabel::OBForceField::ScreenByRMSD(double, double, short int, OpenBabel::OBBitVec, bool)’ at ./src/confsearch.cpp:669:28: 2023-09-12T10:53:52,994 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:52,994 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:52,995 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:52,996 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:52,997 inlined from ‘int OpenBabel::OBForceField::ScreenByRMSD(double, double, short int, OpenBabel::OBBitVec, bool)’ at ./src/confsearch.cpp:679:32: 2023-09-12T10:53:52,997 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:53:52,998 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:52,999 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:54,346 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/confsearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:53:54,347 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/confsearch.o /tmp/ccyRf2iW.s 2023-09-12T10:53:54,351 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:55,284 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:53:55,285 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:53:55,286 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/confsearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/confsearch.' 2023-09-12T10:53:55,290 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/data.cpp -o build/temp.linux-armv7l-cpython-311/./src/data.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:53:55,293 Using built-in specs. 2023-09-12T10:53:55,294 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:55,295 Target: arm-linux-gnueabihf 2023-09-12T10:53:55,295 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:53:55,296 Thread model: posix 2023-09-12T10:53:55,296 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:55,297 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:55,297 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/data.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:53:55,298 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/data.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase data.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccvW8CBm.s 2023-09-12T10:53:55,307 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:55,307 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:55,308 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:55,309 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:55,310 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:55,310 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:55,311 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:55,312 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:55,312 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:55,313 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:55,313 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:55,313 #include "..." search starts here: 2023-09-12T10:53:55,314 #include <...> search starts here: 2023-09-12T10:53:55,314 /usr/include/eigen3 2023-09-12T10:53:55,315 include 2023-09-12T10:53:55,315 /usr/include/python3.11 2023-09-12T10:53:55,316 /usr/include/c++/12 2023-09-12T10:53:55,316 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:55,316 /usr/include/c++/12/backward 2023-09-12T10:53:55,317 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:55,317 /usr/local/include 2023-09-12T10:53:55,318 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:55,318 /usr/include 2023-09-12T10:53:55,318 End of search list. 2023-09-12T10:53:55,319 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:55,319 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:55,320 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:55,321 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:55,325 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:57,037 In file included from include/openbabel/atom.h:33, 2023-09-12T10:53:57,037 from include/openbabel/mol.h:43, 2023-09-12T10:53:57,038 from include/openbabel/data_utilities.h:25, 2023-09-12T10:53:57,038 from ./src/data.cpp:22: 2023-09-12T10:53:57,039 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:57,040 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:57,040 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:57,041 | ^ 2023-09-12T10:53:57,042 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,043 37 | # define UNUSED(x) x 2023-09-12T10:53:57,044 | ^ 2023-09-12T10:53:57,710 In file included from include/openbabel/mol.h:52: 2023-09-12T10:53:57,711 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:57,712 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:57,712 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:57,713 | ^ 2023-09-12T10:53:57,714 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:57,715 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:57,715 | ^~~~~~~~ 2023-09-12T10:53:57,716 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:57,717 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:57,718 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:57,719 | ^ 2023-09-12T10:53:57,719 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:57,720 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:57,720 | ^~~~~~~~ 2023-09-12T10:53:57,735 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:57,735 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:57,736 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:57,737 | ^ 2023-09-12T10:53:57,737 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:57,738 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:57,738 | ^~~~~~~~ 2023-09-12T10:53:57,741 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:57,742 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:57,742 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:57,743 | ^ 2023-09-12T10:53:57,744 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:57,744 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:57,745 | ^~~~~~~~ 2023-09-12T10:53:58,480 ./src/data.cpp: In member function ‘bool OpenBabel::OBResidueData::AssignBonds(OpenBabel::OBMol&, OpenBabel::OBBitVec&)’: 2023-09-12T10:53:58,481 ./src/data.cpp:810:56: warning: unused parameter ‘bv’ [-Wunused-parameter] 2023-09-12T10:53:58,482 810 | bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &bv) 2023-09-12T10:53:58,482 | ~~~~~~~~~~^~ 2023-09-12T10:54:05,542 In file included from ./src/data.cpp:21: 2023-09-12T10:54:05,543 In constructor ‘OpenBabel::OBElement::OBElement(int, const char*, double, double, double, int, double, double, double, double, double, double, double, std::string)’, 2023-09-12T10:54:05,544 inlined from ‘virtual void OpenBabel::OBElementTable::ParseLine(const char*)’ at ./src/data.cpp:117:79: 2023-09-12T10:54:05,544 include/openbabel/data.h:118:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 3 bytes from a string of length 3 [-Wstringop-truncation] 2023-09-12T10:54:05,545 118 | strncpy(_symbol, sym, 3); // Make sure to leave 4th character for null 2023-09-12T10:54:05,546 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:54:05,635 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:54:05,635 from include/openbabel/data.h:28: 2023-09-12T10:54:05,636 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]’: 2023-09-12T10:54:05,637 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:54:05,638 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:05,639 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:05,894 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:54:05,895 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:05,896 inlined from ‘virtual void OpenBabel::OBIsotopeTable::ParseLine(const char*)’ at ./src/data.cpp:393:30: 2023-09-12T10:54:05,896 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:05,897 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:05,898 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:06,022 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:54:06,023 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:06,023 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:06,024 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,082 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:06,083 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:06,083 inlined from ‘std::vector OpenBabel::OBElementTable::GetRGB(int)’ at ./src/data.cpp:210:25: 2023-09-12T10:54:06,084 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:06,084 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:06,085 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,086 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:06,086 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:06,087 inlined from ‘std::vector OpenBabel::OBElementTable::GetRGB(int)’ at ./src/data.cpp:216:21: 2023-09-12T10:54:06,088 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:06,089 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:06,089 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,947 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBAtomHOF&}; _Tp = OpenBabel::OBAtomHOF; _Alloc = std::allocator]’: 2023-09-12T10:54:07,948 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:07,948 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:07,949 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:08,194 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBAtomHOF; _Alloc = std::allocator]’, 2023-09-12T10:54:08,195 inlined from ‘virtual void OpenBabel::OBAtomicHeatOfFormationTable::ParseLine(const char*)’ at ./src/data.cpp:490:31: 2023-09-12T10:54:08,195 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:08,196 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:08,196 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:08,938 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/data.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:54:08,939 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/data.o /tmp/ccvW8CBm.s 2023-09-12T10:54:08,947 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:10,002 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:10,003 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:10,003 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/data.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/data.' 2023-09-12T10:54:10,008 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/data_utilities.cpp -o build/temp.linux-armv7l-cpython-311/./src/data_utilities.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:10,012 Using built-in specs. 2023-09-12T10:54:10,013 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:10,013 Target: arm-linux-gnueabihf 2023-09-12T10:54:10,014 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:10,015 Thread model: posix 2023-09-12T10:54:10,015 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:10,016 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:10,016 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/data_utilities.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:54:10,017 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/data_utilities.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase data_utilities.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc8Lk3yA.s 2023-09-12T10:54:10,026 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:10,026 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:10,027 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:10,028 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:10,029 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:10,029 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:10,030 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:10,031 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:10,032 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:10,032 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:10,033 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:10,033 #include "..." search starts here: 2023-09-12T10:54:10,034 #include <...> search starts here: 2023-09-12T10:54:10,035 /usr/include/eigen3 2023-09-12T10:54:10,035 include 2023-09-12T10:54:10,036 /usr/include/python3.11 2023-09-12T10:54:10,036 /usr/include/c++/12 2023-09-12T10:54:10,037 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:10,038 /usr/include/c++/12/backward 2023-09-12T10:54:10,038 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:10,039 /usr/local/include 2023-09-12T10:54:10,039 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:10,040 /usr/include 2023-09-12T10:54:10,040 End of search list. 2023-09-12T10:54:10,041 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:10,042 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:10,043 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:10,044 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:10,046 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:11,598 In file included from include/openbabel/atom.h:33, 2023-09-12T10:54:11,598 from include/openbabel/mol.h:43, 2023-09-12T10:54:11,599 from include/openbabel/data_utilities.h:25, 2023-09-12T10:54:11,599 from ./src/data_utilities.cpp:23: 2023-09-12T10:54:11,600 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:11,601 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:11,601 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:11,602 | ^ 2023-09-12T10:54:11,602 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:11,603 37 | # define UNUSED(x) x 2023-09-12T10:54:11,603 | ^ 2023-09-12T10:54:12,375 In file included from include/openbabel/mol.h:52: 2023-09-12T10:54:12,375 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:12,376 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:12,376 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:12,377 | ^ 2023-09-12T10:54:12,378 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:12,379 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:12,379 | ^~~~~~~~ 2023-09-12T10:54:12,380 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:12,381 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:12,382 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:12,383 | ^ 2023-09-12T10:54:12,383 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:12,384 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:12,385 | ^~~~~~~~ 2023-09-12T10:54:12,400 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:12,401 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:12,401 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:12,402 | ^ 2023-09-12T10:54:12,403 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:12,403 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:12,404 | ^~~~~~~~ 2023-09-12T10:54:12,407 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:12,408 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:12,408 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:12,409 | ^ 2023-09-12T10:54:12,410 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:12,410 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:12,411 | ^~~~~~~~ 2023-09-12T10:54:12,712 ./src/data_utilities.cpp: In function ‘bool OpenBabel::extract_thermochemistry(OBMol&, bool, int*, int, double, double*, double*, double*, double*, double*, double*, double*, double*, std::vector&)’: 2023-09-12T10:54:12,713 ./src/data_utilities.cpp:121:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:54:12,713 121 | for(int i = 0; (i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:54:14,103 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:14,104 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:14,105 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:14,291 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:54:14,292 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:14,292 inlined from ‘bool OpenBabel::extract_thermochemistry(OBMol&, bool, int*, int, double, double*, double*, double*, double*, double*, double*, double*, double*, std::vector&)’ at ./src/data_utilities.cpp:175:26: 2023-09-12T10:54:14,293 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:14,294 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:14,295 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:14,295 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:14,296 inlined from ‘bool OpenBabel::extract_thermochemistry(OBMol&, bool, int*, int, double, double*, double*, double*, double*, double*, double*, double*, double*, std::vector&)’ at ./src/data_utilities.cpp:176:26: 2023-09-12T10:54:14,297 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:14,298 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:14,298 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:14,299 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:14,300 inlined from ‘bool OpenBabel::extract_thermochemistry(OBMol&, bool, int*, int, double, double*, double*, double*, double*, double*, double*, double*, double*, std::vector&)’ at ./src/data_utilities.cpp:177:26: 2023-09-12T10:54:14,301 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:14,301 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:14,302 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:14,302 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:14,303 inlined from ‘bool OpenBabel::extract_thermochemistry(OBMol&, bool, int*, int, double, double*, double*, double*, double*, double*, double*, double*, double*, std::vector&)’ at ./src/data_utilities.cpp:178:26: 2023-09-12T10:54:14,304 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:14,304 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:14,305 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:14,305 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:14,306 inlined from ‘bool OpenBabel::extract_thermochemistry(OBMol&, bool, int*, int, double, double*, double*, double*, double*, double*, double*, double*, double*, std::vector&)’ at ./src/data_utilities.cpp:179:26: 2023-09-12T10:54:14,307 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:54:14,307 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:14,308 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:14,645 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/data_utilities.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:54:14,646 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/data_utilities.o /tmp/cc8Lk3yA.s 2023-09-12T10:54:14,650 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:14,738 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:14,739 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:14,740 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/data_utilities.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/data_utilities.' 2023-09-12T10:54:14,741 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/depict/asciipainter.cpp -o build/temp.linux-armv7l-cpython-311/./src/depict/asciipainter.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:14,745 Using built-in specs. 2023-09-12T10:54:14,746 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:14,746 Target: arm-linux-gnueabihf 2023-09-12T10:54:14,746 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:14,747 Thread model: posix 2023-09-12T10:54:14,747 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:14,748 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:14,748 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/asciipainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/' 2023-09-12T10:54:14,749 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/depict/asciipainter.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/depict/ -dumpbase asciipainter.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccbzlZ0S.s 2023-09-12T10:54:14,758 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:14,759 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:14,760 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:14,760 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:14,761 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:14,762 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:14,762 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:14,763 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:14,763 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:14,764 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:14,765 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:14,766 #include "..." search starts here: 2023-09-12T10:54:14,766 #include <...> search starts here: 2023-09-12T10:54:14,766 /usr/include/eigen3 2023-09-12T10:54:14,767 include 2023-09-12T10:54:14,767 /usr/include/python3.11 2023-09-12T10:54:14,768 /usr/include/c++/12 2023-09-12T10:54:14,768 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:14,768 /usr/include/c++/12/backward 2023-09-12T10:54:14,769 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:14,769 /usr/local/include 2023-09-12T10:54:14,770 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:14,770 /usr/include 2023-09-12T10:54:14,770 End of search list. 2023-09-12T10:54:14,771 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:14,771 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:14,772 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:14,773 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:14,778 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:16,033 In file included from ./src/depict/asciipainter.cpp:19: 2023-09-12T10:54:16,034 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2023-09-12T10:54:16,035 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T10:54:16,035 34 | void SetFontFamily(const std::string &fontFamily) {} 2023-09-12T10:54:16,036 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:54:16,048 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontSize(int)’: 2023-09-12T10:54:16,049 ./src/depict/asciipainter.cpp:54:38: warning: unused parameter ‘pointSize’ [-Wunused-parameter] 2023-09-12T10:54:16,049 54 | void ASCIIPainter::SetFontSize(int pointSize) 2023-09-12T10:54:16,050 | ~~~~^~~~~~~~~ 2023-09-12T10:54:16,050 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillColor(const OpenBabel::OBColor&)’: 2023-09-12T10:54:16,051 ./src/depict/asciipainter.cpp:58:50: warning: unused parameter ‘color’ [-Wunused-parameter] 2023-09-12T10:54:16,052 58 | void ASCIIPainter::SetFillColor(const OBColor &color) 2023-09-12T10:54:16,052 | ~~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:54:16,053 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillRadial(const OpenBabel::OBColor&, const OpenBabel::OBColor&)’: 2023-09-12T10:54:16,054 ./src/depict/asciipainter.cpp:62:51: warning: unused parameter ‘start’ [-Wunused-parameter] 2023-09-12T10:54:16,054 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2023-09-12T10:54:16,055 | ~~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:54:16,055 ./src/depict/asciipainter.cpp:62:73: warning: unused parameter ‘end’ [-Wunused-parameter] 2023-09-12T10:54:16,056 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2023-09-12T10:54:16,057 | ~~~~~~~~~~~~~~~^~~ 2023-09-12T10:54:16,057 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenColor(const OpenBabel::OBColor&)’: 2023-09-12T10:54:16,058 ./src/depict/asciipainter.cpp:67:49: warning: unused parameter ‘color’ [-Wunused-parameter] 2023-09-12T10:54:16,059 67 | void ASCIIPainter::SetPenColor(const OBColor &color) 2023-09-12T10:54:16,059 | ~~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:54:16,060 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenWidth(double)’: 2023-09-12T10:54:16,061 ./src/depict/asciipainter.cpp:71:41: warning: unused parameter ‘width’ [-Wunused-parameter] 2023-09-12T10:54:16,062 71 | void ASCIIPainter::SetPenWidth(double width) 2023-09-12T10:54:16,062 | ~~~~~~~^~~~~ 2023-09-12T10:54:16,076 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawLine(double, double, double, double, const std::vector&)’: 2023-09-12T10:54:16,076 ./src/depict/asciipainter.cpp:80:103: warning: unused parameter ‘dashes’ [-Wunused-parameter] 2023-09-12T10:54:16,077 80 | void ASCIIPainter::DrawLine(double x1, double y1, double x2, double y2, const std::vector & dashes) 2023-09-12T10:54:16,077 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-09-12T10:54:16,097 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawCircle(double, double, double)’: 2023-09-12T10:54:16,097 ./src/depict/asciipainter.cpp:106:40: warning: unused parameter ‘x’ [-Wunused-parameter] 2023-09-12T10:54:16,098 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2023-09-12T10:54:16,098 | ~~~~~~~^ 2023-09-12T10:54:16,099 ./src/depict/asciipainter.cpp:106:50: warning: unused parameter ‘y’ [-Wunused-parameter] 2023-09-12T10:54:16,100 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2023-09-12T10:54:16,100 | ~~~~~~~^ 2023-09-12T10:54:16,101 ./src/depict/asciipainter.cpp:106:60: warning: unused parameter ‘r’ [-Wunused-parameter] 2023-09-12T10:54:16,101 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2023-09-12T10:54:16,102 | ~~~~~~~^ 2023-09-12T10:54:16,103 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawBall(double, double, double, double)’: 2023-09-12T10:54:16,104 ./src/depict/asciipainter.cpp:110:38: warning: unused parameter ‘x’ [-Wunused-parameter] 2023-09-12T10:54:16,104 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:54:16,105 | ~~~~~~~^ 2023-09-12T10:54:16,106 ./src/depict/asciipainter.cpp:110:48: warning: unused parameter ‘y’ [-Wunused-parameter] 2023-09-12T10:54:16,106 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:54:16,107 | ~~~~~~~^ 2023-09-12T10:54:16,108 ./src/depict/asciipainter.cpp:110:58: warning: unused parameter ‘r’ [-Wunused-parameter] 2023-09-12T10:54:16,108 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:54:16,109 | ~~~~~~~^ 2023-09-12T10:54:16,110 ./src/depict/asciipainter.cpp:110:68: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2023-09-12T10:54:16,111 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:54:16,111 | ~~~~~~~^~~~~~~ 2023-09-12T10:54:16,112 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawText(double, double, const std::string&)’: 2023-09-12T10:54:16,113 ./src/depict/asciipainter.cpp:118:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:54:16,113 118 | for (int i=0; i search starts here: 2023-09-12T10:54:18,234 /usr/include/eigen3 2023-09-12T10:54:18,235 include 2023-09-12T10:54:18,236 /usr/include/python3.11 2023-09-12T10:54:18,236 /usr/include/c++/12 2023-09-12T10:54:18,237 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:18,238 /usr/include/c++/12/backward 2023-09-12T10:54:18,238 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:18,239 /usr/local/include 2023-09-12T10:54:18,239 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:18,240 /usr/include 2023-09-12T10:54:18,241 End of search list. 2023-09-12T10:54:18,241 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:18,242 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:18,243 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:18,243 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:18,246 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:19,490 In file included from ./src/depict/commandpainter.cpp:19: 2023-09-12T10:54:19,490 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2023-09-12T10:54:19,491 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T10:54:19,492 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2023-09-12T10:54:19,493 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:54:19,539 ./src/depict/commandpainter.cpp: In member function ‘virtual void OpenBabel::CommandPainter::DrawBall(double, double, double, double)’: 2023-09-12T10:54:19,540 ./src/depict/commandpainter.cpp:115:70: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2023-09-12T10:54:19,541 115 | void CommandPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:54:19,541 | ~~~~~~~^~~~~~~ 2023-09-12T10:54:19,543 ./src/depict/commandpainter.cpp: In member function ‘virtual OpenBabel::OBFontMetrics OpenBabel::CommandPainter::GetFontMetrics(const std::string&)’: 2023-09-12T10:54:19,544 ./src/depict/commandpainter.cpp:125:67: warning: unused parameter ‘text’ [-Wunused-parameter] 2023-09-12T10:54:19,545 125 | OBFontMetrics CommandPainter::GetFontMetrics(const std::string &text) 2023-09-12T10:54:19,545 | ~~~~~~~~~~~~~~~~~~~^~~~ 2023-09-12T10:54:20,201 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/commandpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/' 2023-09-12T10:54:20,201 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/depict/commandpainter.o /tmp/ccAjByGc.s 2023-09-12T10:54:20,205 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:20,271 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:20,272 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:20,272 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/commandpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/commandpainter.' 2023-09-12T10:54:20,273 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/depict/depict.cpp -o build/temp.linux-armv7l-cpython-311/./src/depict/depict.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:20,277 Using built-in specs. 2023-09-12T10:54:20,278 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:20,279 Target: arm-linux-gnueabihf 2023-09-12T10:54:20,279 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:20,280 Thread model: posix 2023-09-12T10:54:20,280 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:20,281 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:20,281 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/depict.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/' 2023-09-12T10:54:20,282 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/depict/depict.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/depict/ -dumpbase depict.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc88oYaf.s 2023-09-12T10:54:20,290 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:20,291 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:20,292 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:20,293 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:20,293 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:20,294 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:20,294 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:20,295 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:20,295 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:20,296 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:20,297 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:20,297 #include "..." search starts here: 2023-09-12T10:54:20,298 #include <...> search starts here: 2023-09-12T10:54:20,298 /usr/include/eigen3 2023-09-12T10:54:20,299 include 2023-09-12T10:54:20,300 /usr/include/python3.11 2023-09-12T10:54:20,300 /usr/include/c++/12 2023-09-12T10:54:20,301 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:20,302 /usr/include/c++/12/backward 2023-09-12T10:54:20,302 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:20,303 /usr/local/include 2023-09-12T10:54:20,304 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:20,305 /usr/include 2023-09-12T10:54:20,305 End of search list. 2023-09-12T10:54:20,306 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:20,306 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:20,307 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:20,307 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:20,312 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:21,931 In file included from include/openbabel/atom.h:33, 2023-09-12T10:54:21,931 from include/openbabel/mol.h:43, 2023-09-12T10:54:21,932 from ./src/depict/depict.cpp:20: 2023-09-12T10:54:21,933 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:21,933 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:21,934 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:21,934 | ^ 2023-09-12T10:54:21,935 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:21,935 37 | # define UNUSED(x) x 2023-09-12T10:54:21,936 | ^ 2023-09-12T10:54:22,699 In file included from include/openbabel/mol.h:52: 2023-09-12T10:54:22,699 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:22,700 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:22,701 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:22,702 | ^ 2023-09-12T10:54:22,702 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:22,703 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:22,704 | ^~~~~~~~ 2023-09-12T10:54:22,705 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:22,706 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:22,707 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:22,707 | ^ 2023-09-12T10:54:22,708 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:22,709 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:22,709 | ^~~~~~~~ 2023-09-12T10:54:22,725 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:22,726 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:22,727 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:22,728 | ^ 2023-09-12T10:54:22,728 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:22,729 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:22,730 | ^~~~~~~~ 2023-09-12T10:54:22,733 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:22,734 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:22,734 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:22,735 | ^ 2023-09-12T10:54:22,735 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:22,736 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:22,736 | ^~~~~~~~ 2023-09-12T10:54:23,322 ./src/depict/depict.cpp: In function ‘unsigned int OpenBabel::GetAtomSymClass(OBAtom*)’: 2023-09-12T10:54:23,322 ./src/depict/depict.cpp:280:11: warning: unused variable ‘nclasses’ [-Wunused-variable] 2023-09-12T10:54:23,323 280 | int nclasses = end_pos - copy_sym.begin(); 2023-09-12T10:54:23,323 | ^~~~~~~~ 2023-09-12T10:54:23,512 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtom(OpenBabel::OBAtom*)’: 2023-09-12T10:54:23,513 ./src/depict/depict.cpp:839:42: warning: unused parameter ‘atom’ [-Wunused-parameter] 2023-09-12T10:54:23,513 839 | void OBDepictPrivate::DrawAtom(OBAtom *atom) 2023-09-12T10:54:23,514 | ~~~~~~~~^~~~ 2023-09-12T10:54:23,522 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtomLabel(const std::string&, int, const OpenBabel::vector3&)’: 2023-09-12T10:54:23,523 ./src/depict/depict.cpp:966:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:54:23,523 966 | OBFontMetrics metrics = painter->GetFontMetrics(str); 2023-09-12T10:54:23,524 | ^~~~~~~ 2023-09-12T10:54:23,525 ./src/depict/depict.cpp:971:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:54:23,526 971 | OBFontMetrics metrics = painter->GetFontMetrics(subscript); 2023-09-12T10:54:23,527 | ^~~~~~~ 2023-09-12T10:54:23,535 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawSimpleBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, int, bool)’: 2023-09-12T10:54:23,536 ./src/depict/depict.cpp:1011:36: warning: unused parameter ‘crossed_bond’ [-Wunused-parameter] 2023-09-12T10:54:23,536 1011 | OBAtom* endAtom, int order, bool crossed_bond) 2023-09-12T10:54:23,537 | ~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:23,555 ./src/depict/depict.cpp: In member function ‘void OpenBabel::OBDepictPrivateBallAndStick::DrawAromaticRingBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, const OpenBabel::vector3&, double)’: 2023-09-12T10:54:23,556 ./src/depict/depict.cpp:1156:99: warning: expression does not compute the number of elements in this array; element type is ‘const float’, not ‘double’ [-Wsizeof-array-div] 2023-09-12T10:54:23,557 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2023-09-12T10:54:23,557 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T10:54:23,558 ./src/depict/depict.cpp:1156:100: note: add parentheses around ‘sizeof (double)’ to silence this warning 2023-09-12T10:54:23,559 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2023-09-12T10:54:23,560 | ^~~~~~~~~~~~~~ 2023-09-12T10:54:23,560 | ( ) 2023-09-12T10:54:23,561 ./src/depict/depict.cpp:1155:24: note: array ‘dashpattern’ declared here 2023-09-12T10:54:23,562 1155 | static const float dashpattern[] = {5., 5.}; 2023-09-12T10:54:23,562 | ^~~~~~~~~~~ 2023-09-12T10:54:23,563 ./src/depict/depict.cpp:1133:152: warning: unused parameter ‘center’ [-Wunused-parameter] 2023-09-12T10:54:23,563 1133 | inline void OBDepictPrivateBallAndStick::DrawAromaticRingBond(OBAtom *prevAtom, OBAtom *beginAtom, OBAtom *endAtom, OBAtom *nextAtom, const vector3 ¢er, double dist) 2023-09-12T10:54:23,564 | ~~~~~~~~~~~~~~~^~~~~~ 2023-09-12T10:54:30,085 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:54:30,085 from include/openbabel/mol.h:35: 2023-09-12T10:54:30,086 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]’: 2023-09-12T10:54:30,087 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:54:30,087 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:30,088 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,138 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: 2023-09-12T10:54:30,138 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:54:30,181 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:30,182 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:30,183 inlined from ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:1052:21: 2023-09-12T10:54:30,184 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,184 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:30,185 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,186 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:30,187 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:30,187 inlined from ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:1053:21: 2023-09-12T10:54:30,188 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,188 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:30,189 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,189 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:30,190 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:30,191 inlined from ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:1055:21: 2023-09-12T10:54:30,191 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,192 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:30,192 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,245 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:30,245 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:30,246 inlined from ‘virtual void OpenBabel::OBDepictPrivate::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:692:21: 2023-09-12T10:54:30,247 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,247 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:30,248 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,248 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:30,249 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:30,250 inlined from ‘virtual void OpenBabel::OBDepictPrivate::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:693:21: 2023-09-12T10:54:30,250 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,251 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:30,252 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,253 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:30,253 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:54:30,254 inlined from ‘virtual void OpenBabel::OBDepictPrivate::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:695:21: 2023-09-12T10:54:30,254 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,255 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:30,255 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,321 In file included from /usr/include/c++/12/algorithm:61, 2023-09-12T10:54:30,321 from include/openbabel/ring.h:24, 2023-09-12T10:54:30,322 from include/openbabel/mol.h:51: 2023-09-12T10:54:30,322 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’: 2023-09-12T10:54:30,323 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,324 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:54:30,324 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,325 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,356 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’: 2023-09-12T10:54:30,357 /usr/include/c++/12/bits/stl_algo.h:82:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,358 82 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, 2023-09-12T10:54:30,358 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,359 /usr/include/c++/12/bits/stl_algo.h:82:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,359 /usr/include/c++/12/bits/stl_algo.h:82:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,360 /usr/include/c++/12/bits/stl_algo.h:82:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,402 In file included from /usr/include/c++/12/bits/stl_algo.h:60: 2023-09-12T10:54:30,403 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’: 2023-09-12T10:54:30,403 /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,404 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T10:54:30,405 | ^~~~~~~~~~~~~ 2023-09-12T10:54:30,475 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’: 2023-09-12T10:54:30,476 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,476 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:54:30,477 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,478 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,478 In function ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’, 2023-09-12T10:54:30,479 inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38: 2023-09-12T10:54:30,480 /usr/include/c++/12/bits/stl_algo.h:1887:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,480 1887 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2023-09-12T10:54:30,481 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:30,482 1888 | __comp); 2023-09-12T10:54:30,482 | ~~~~~~~ 2023-09-12T10:54:30,483 /usr/include/c++/12/bits/stl_algo.h:1887:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,484 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’: 2023-09-12T10:54:30,484 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:30,485 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:54:30,486 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:31,266 ./src/depict/depict.cpp: In member function ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’: 2023-09-12T10:54:31,266 ./src/depict/depict.cpp:423:25: warning: ‘max_z’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:31,267 423 | d->zScale = max_z - min_z; 2023-09-12T10:54:31,267 | ~~~~~~^~~~~~~ 2023-09-12T10:54:31,268 ./src/depict/depict.cpp:395:21: note: ‘max_z’ was declared here 2023-09-12T10:54:31,269 395 | double min_z, max_z; 2023-09-12T10:54:31,269 | ^~~~~ 2023-09-12T10:54:31,270 ./src/depict/depict.cpp:423:25: warning: ‘min_z’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:31,271 423 | d->zScale = max_z - min_z; 2023-09-12T10:54:31,271 | ~~~~~~^~~~~~~ 2023-09-12T10:54:31,272 ./src/depict/depict.cpp:395:14: note: ‘min_z’ was declared here 2023-09-12T10:54:31,273 395 | double min_z, max_z; 2023-09-12T10:54:31,274 | ^~~~~ 2023-09-12T10:54:31,274 ./src/depict/depict.cpp:421:22: warning: ‘max_y’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:31,275 421 | height = max_y - min_y + 2*margin; 2023-09-12T10:54:31,276 | ~~~~~~^~~~~~~ 2023-09-12T10:54:31,277 ./src/depict/depict.cpp:394:21: note: ‘max_y’ was declared here 2023-09-12T10:54:31,278 394 | double min_y, max_y; 2023-09-12T10:54:31,278 | ^~~~~ 2023-09-12T10:54:31,279 ./src/depict/depict.cpp:421:22: warning: ‘min_y’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:31,280 421 | height = max_y - min_y + 2*margin; 2023-09-12T10:54:31,281 | ~~~~~~^~~~~~~ 2023-09-12T10:54:31,282 ./src/depict/depict.cpp:394:14: note: ‘min_y’ was declared here 2023-09-12T10:54:31,283 394 | double min_y, max_y; 2023-09-12T10:54:31,284 | ^~~~~ 2023-09-12T10:54:31,284 ./src/depict/depict.cpp:420:22: warning: ‘max_x’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:31,285 420 | width = max_x - min_x + 2*margin; 2023-09-12T10:54:31,286 | ~~~~~~^~~~~~~ 2023-09-12T10:54:31,287 ./src/depict/depict.cpp:393:21: note: ‘max_x’ was declared here 2023-09-12T10:54:31,287 393 | double min_x, max_x; 2023-09-12T10:54:31,288 | ^~~~~ 2023-09-12T10:54:31,289 ./src/depict/depict.cpp:420:22: warning: ‘min_x’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:31,290 420 | width = max_x - min_x + 2*margin; 2023-09-12T10:54:31,290 | ~~~~~~^~~~~~~ 2023-09-12T10:54:31,291 ./src/depict/depict.cpp:393:14: note: ‘min_x’ was declared here 2023-09-12T10:54:31,292 393 | double min_x, max_x; 2023-09-12T10:54:31,293 | ^~~~~ 2023-09-12T10:54:31,314 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:54:31,315 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:54:31,315 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:511:31: 2023-09-12T10:54:31,316 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:31,317 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:31,318 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:31,318 In function ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’, 2023-09-12T10:54:31,319 inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38, 2023-09-12T10:54:31,319 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1937:25, 2023-09-12T10:54:31,320 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = bool (*)(const pair&, const pair&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:54:31,321 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2023-09-12T10:54:31,321 /usr/include/c++/12/bits/stl_algo.h:1887:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:31,322 1887 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2023-09-12T10:54:31,323 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:31,324 1888 | __comp); 2023-09-12T10:54:31,324 | ~~~~~~~ 2023-09-12T10:54:31,325 /usr/include/c++/12/bits/stl_algo.h:1887:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:31,326 In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’, 2023-09-12T10:54:31,326 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1937:25, 2023-09-12T10:54:31,327 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = bool (*)(const pair&, const pair&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:54:31,328 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2023-09-12T10:54:31,328 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:31,329 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:54:31,329 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:31,330 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’, 2023-09-12T10:54:31,330 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const pair&)>]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-12T10:54:31,331 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = bool (*)(const pair&, const pair&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, 2023-09-12T10:54:31,331 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2023-09-12T10:54:31,332 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:31,333 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:54:31,334 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:31,334 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:54:31,335 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:54:31,336 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,810 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/depict.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/' 2023-09-12T10:54:33,811 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/depict/depict.o /tmp/cc88oYaf.s 2023-09-12T10:54:33,816 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:34,557 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:34,558 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:34,558 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/depict.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/depict.' 2023-09-12T10:54:34,562 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/depict/svgpainter.cpp -o build/temp.linux-armv7l-cpython-311/./src/depict/svgpainter.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:34,566 Using built-in specs. 2023-09-12T10:54:34,566 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:34,567 Target: arm-linux-gnueabihf 2023-09-12T10:54:34,567 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:34,568 Thread model: posix 2023-09-12T10:54:34,569 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:34,569 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:34,570 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/svgpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/' 2023-09-12T10:54:34,570 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/depict/svgpainter.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/depict/ -dumpbase svgpainter.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccweSers.s 2023-09-12T10:54:34,579 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:34,580 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:34,581 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:34,581 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:34,581 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:34,582 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:34,582 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:34,583 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:34,583 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:34,584 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:34,584 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:34,584 #include "..." search starts here: 2023-09-12T10:54:34,585 #include <...> search starts here: 2023-09-12T10:54:34,585 /usr/include/eigen3 2023-09-12T10:54:34,586 include 2023-09-12T10:54:34,586 /usr/include/python3.11 2023-09-12T10:54:34,587 /usr/include/c++/12 2023-09-12T10:54:34,588 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:34,588 /usr/include/c++/12/backward 2023-09-12T10:54:34,588 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:34,589 /usr/local/include 2023-09-12T10:54:34,589 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:34,590 /usr/include 2023-09-12T10:54:34,590 End of search list. 2023-09-12T10:54:34,591 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:34,591 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:34,593 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:34,593 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:34,598 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:36,087 In file included from ./src/depict/svgpainter.cpp:18: 2023-09-12T10:54:36,087 include/openbabel/depict/svgpainter.h: In constructor ‘OpenBabel::SVGPainter::SVGPainter(std::ostream&, std::set >*, bool, double, double)’: 2023-09-12T10:54:36,088 include/openbabel/depict/svgpainter.h:77:11: warning: ‘OpenBabel::SVGPainter::m_fontPointSize’ will be initialized after [-Wreorder] 2023-09-12T10:54:36,089 77 | int m_fontPointSize; 2023-09-12T10:54:36,089 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:36,090 include/openbabel/depict/svgpainter.h:75:12: warning: ‘bool OpenBabel::SVGPainter::m_isFillcolor’ [-Wreorder] 2023-09-12T10:54:36,091 75 | bool m_isFillcolor; 2023-09-12T10:54:36,091 | ^~~~~~~~~~~~~ 2023-09-12T10:54:36,092 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2023-09-12T10:54:36,093 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2023-09-12T10:54:36,094 | ^~~~~~~~~~ 2023-09-12T10:54:36,094 include/openbabel/depict/svgpainter.h:75:12: warning: ‘OpenBabel::SVGPainter::m_isFillcolor’ will be initialized after [-Wreorder] 2023-09-12T10:54:36,095 75 | bool m_isFillcolor; 2023-09-12T10:54:36,096 | ^~~~~~~~~~~~~ 2023-09-12T10:54:36,097 include/openbabel/depict/svgpainter.h:74:32: warning: ‘std::set >* OpenBabel::SVGPainter::m_Gradients’ [-Wreorder] 2023-09-12T10:54:36,097 74 | std::set *m_Gradients; 2023-09-12T10:54:36,098 | ^~~~~~~~~~~ 2023-09-12T10:54:36,099 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2023-09-12T10:54:36,099 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2023-09-12T10:54:36,100 | ^~~~~~~~~~ 2023-09-12T10:54:36,189 ./src/depict/svgpainter.cpp: In member function ‘void OpenBabel::SVGPainter::WriteImage(const std::string&)’: 2023-09-12T10:54:36,190 ./src/depict/svgpainter.cpp:172:50: warning: unused parameter ‘filename’ [-Wunused-parameter] 2023-09-12T10:54:36,190 172 | void SVGPainter::WriteImage(const std::string &filename) 2023-09-12T10:54:36,191 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ 2023-09-12T10:54:38,161 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/svgpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/' 2023-09-12T10:54:38,161 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/depict/svgpainter.o /tmp/ccweSers.s 2023-09-12T10:54:38,166 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:38,349 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:38,349 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:38,350 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/depict/svgpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/depict/svgpainter.' 2023-09-12T10:54:38,351 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/descriptor.cpp -o build/temp.linux-armv7l-cpython-311/./src/descriptor.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:38,355 Using built-in specs. 2023-09-12T10:54:38,356 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:38,357 Target: arm-linux-gnueabihf 2023-09-12T10:54:38,357 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:38,358 Thread model: posix 2023-09-12T10:54:38,359 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:38,359 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:38,360 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:54:38,360 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptor.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase descriptor.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccGUy2st.s 2023-09-12T10:54:38,369 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:38,370 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:38,371 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:38,371 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:38,372 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:38,373 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:38,373 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:38,374 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:38,375 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:38,375 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:38,376 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:38,376 #include "..." search starts here: 2023-09-12T10:54:38,377 #include <...> search starts here: 2023-09-12T10:54:38,377 /usr/include/eigen3 2023-09-12T10:54:38,378 include 2023-09-12T10:54:38,379 /usr/include/python3.11 2023-09-12T10:54:38,379 /usr/include/c++/12 2023-09-12T10:54:38,380 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:38,380 /usr/include/c++/12/backward 2023-09-12T10:54:38,381 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:38,382 /usr/local/include 2023-09-12T10:54:38,382 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:38,383 /usr/include 2023-09-12T10:54:38,383 End of search list. 2023-09-12T10:54:38,384 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:38,384 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:38,386 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:38,386 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:38,391 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:40,070 In file included from include/openbabel/generic.h:31, 2023-09-12T10:54:40,070 from ./src/descriptor.cpp:21: 2023-09-12T10:54:40,071 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:40,072 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:40,072 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:40,073 | ^ 2023-09-12T10:54:40,073 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,074 37 | # define UNUSED(x) x 2023-09-12T10:54:40,075 | ^ 2023-09-12T10:54:40,277 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,278 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,278 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:40,279 | ^ 2023-09-12T10:54:40,280 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:40,280 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:40,281 | ^~~~~~~~ 2023-09-12T10:54:40,283 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,284 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,285 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:40,286 | ^ 2023-09-12T10:54:40,287 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:40,287 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:40,288 | ^~~~~~~~ 2023-09-12T10:54:40,303 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,304 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,305 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:40,306 | ^ 2023-09-12T10:54:40,306 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:40,307 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:40,308 | ^~~~~~~~ 2023-09-12T10:54:40,311 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,312 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,313 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:40,313 | ^ 2023-09-12T10:54:40,314 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:40,314 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:40,315 | ^~~~~~~~ 2023-09-12T10:54:40,392 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:54:40,393 from ./src/descriptor.cpp:23: 2023-09-12T10:54:40,393 include/openbabel/plugin.h: At global scope: 2023-09-12T10:54:40,394 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:40,395 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:40,395 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:40,396 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:54:40,396 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:54:40,397 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:54:40,398 from /usr/include/c++/12/ios:42, 2023-09-12T10:54:40,398 from /usr/include/c++/12/istream:38, 2023-09-12T10:54:40,399 from /usr/include/c++/12/sstream:38, 2023-09-12T10:54:40,400 from include/openbabel/oberror.h:26, 2023-09-12T10:54:40,400 from ./src/descriptor.cpp:20: 2023-09-12T10:54:40,401 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:40,402 131 | struct binary_function 2023-09-12T10:54:40,402 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:44,338 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:54:44,339 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/descriptor.o /tmp/ccGUy2st.s 2023-09-12T10:54:44,343 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:44,677 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:44,678 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:44,678 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptor.' 2023-09-12T10:54:44,680 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/descriptors/cansmidescriptor.cpp -o build/temp.linux-armv7l-cpython-311/./src/descriptors/cansmidescriptor.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:44,684 Using built-in specs. 2023-09-12T10:54:44,685 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:44,686 Target: arm-linux-gnueabihf 2023-09-12T10:54:44,686 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:44,687 Thread model: posix 2023-09-12T10:54:44,687 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:44,688 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:44,688 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cansmidescriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:54:44,689 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/cansmidescriptor.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/descriptors/ -dumpbase cansmidescriptor.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccn9Q0CU.s 2023-09-12T10:54:44,697 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:44,698 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:44,699 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:44,700 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:44,700 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:44,701 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:44,702 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:44,703 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:44,703 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:44,704 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:44,704 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:44,704 #include "..." search starts here: 2023-09-12T10:54:44,705 #include <...> search starts here: 2023-09-12T10:54:44,705 /usr/include/eigen3 2023-09-12T10:54:44,706 include 2023-09-12T10:54:44,706 /usr/include/python3.11 2023-09-12T10:54:44,706 /usr/include/c++/12 2023-09-12T10:54:44,707 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:44,707 /usr/include/c++/12/backward 2023-09-12T10:54:44,708 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:44,708 /usr/local/include 2023-09-12T10:54:44,709 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:44,709 /usr/include 2023-09-12T10:54:44,710 End of search list. 2023-09-12T10:54:44,710 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:44,711 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:44,712 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:44,712 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:44,719 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:46,166 In file included from include/openbabel/format.h:22, 2023-09-12T10:54:46,167 from include/openbabel/obconversion.h:37, 2023-09-12T10:54:46,168 from ./src/descriptors/cansmidescriptor.cpp:22: 2023-09-12T10:54:46,168 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:46,169 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:46,170 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:46,170 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:54:46,171 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:54:46,172 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:54:46,173 from /usr/include/c++/12/ios:42, 2023-09-12T10:54:46,173 from /usr/include/c++/12/istream:38, 2023-09-12T10:54:46,174 from /usr/include/c++/12/sstream:38, 2023-09-12T10:54:46,175 from include/openbabel/oberror.h:26, 2023-09-12T10:54:46,176 from ./src/descriptors/cansmidescriptor.cpp:20: 2023-09-12T10:54:46,176 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:46,177 131 | struct binary_function 2023-09-12T10:54:46,177 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:46,347 ./src/descriptors/cansmidescriptor.cpp: In member function ‘virtual bool OpenBabel::CanSmiles::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2023-09-12T10:54:46,347 ./src/descriptors/cansmidescriptor.cpp:42:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:54:46,348 42 | bool CanSmiles::Compare(OBBase* pOb, istream& optionText, bool noEval, string* param) 2023-09-12T10:54:46,349 | ~~~~~~~~^~~~~ 2023-09-12T10:54:47,548 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cansmidescriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:54:47,548 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/descriptors/cansmidescriptor.o /tmp/ccn9Q0CU.s 2023-09-12T10:54:47,554 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:47,655 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:47,655 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:47,656 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cansmidescriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cansmidescriptor.' 2023-09-12T10:54:47,656 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/descriptors/cmpdfilter.cpp -o build/temp.linux-armv7l-cpython-311/./src/descriptors/cmpdfilter.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:47,660 Using built-in specs. 2023-09-12T10:54:47,661 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:47,662 Target: arm-linux-gnueabihf 2023-09-12T10:54:47,662 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:47,663 Thread model: posix 2023-09-12T10:54:47,664 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:47,664 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:47,665 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cmpdfilter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:54:47,665 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/cmpdfilter.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/descriptors/ -dumpbase cmpdfilter.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccI3qUMY.s 2023-09-12T10:54:47,674 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:47,675 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:47,675 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:47,676 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:47,676 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:47,677 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:47,677 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:47,678 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:47,678 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:47,679 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:47,680 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:47,680 #include "..." search starts here: 2023-09-12T10:54:47,681 #include <...> search starts here: 2023-09-12T10:54:47,681 /usr/include/eigen3 2023-09-12T10:54:47,682 include 2023-09-12T10:54:47,682 /usr/include/python3.11 2023-09-12T10:54:47,683 /usr/include/c++/12 2023-09-12T10:54:47,684 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:47,684 /usr/include/c++/12/backward 2023-09-12T10:54:47,685 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:47,686 /usr/local/include 2023-09-12T10:54:47,686 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:47,687 /usr/include 2023-09-12T10:54:47,688 End of search list. 2023-09-12T10:54:47,689 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:47,689 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:47,691 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:47,691 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:47,692 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:49,067 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:54:49,068 from ./src/descriptors/cmpdfilter.cpp:21: 2023-09-12T10:54:49,068 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:49,069 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:49,070 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:49,071 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:54:49,071 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:54:49,072 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:54:49,073 from /usr/include/c++/12/ios:42, 2023-09-12T10:54:49,074 from /usr/include/c++/12/istream:38, 2023-09-12T10:54:49,075 from /usr/include/c++/12/sstream:38, 2023-09-12T10:54:49,075 from include/openbabel/oberror.h:26, 2023-09-12T10:54:49,076 from ./src/descriptors/cmpdfilter.cpp:20: 2023-09-12T10:54:49,076 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:49,077 131 | struct binary_function 2023-09-12T10:54:49,077 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:49,127 ./src/descriptors/cmpdfilter.cpp: In member function ‘virtual bool OpenBabel::CompoundFilter::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2023-09-12T10:54:49,128 ./src/descriptors/cmpdfilter.cpp:74:68: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:54:49,128 74 | virtual bool Compare(OBBase* pOb, istream&, bool noEval, string* param) 2023-09-12T10:54:49,129 | ~~~~~~~~^~~~~ 2023-09-12T10:54:50,413 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cmpdfilter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:54:50,413 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/descriptors/cmpdfilter.o /tmp/ccI3qUMY.s 2023-09-12T10:54:50,418 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:50,527 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:50,527 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:50,528 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cmpdfilter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/cmpdfilter.' 2023-09-12T10:54:50,529 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/descriptors/filters.cpp -o build/temp.linux-armv7l-cpython-311/./src/descriptors/filters.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:50,533 Using built-in specs. 2023-09-12T10:54:50,534 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:50,534 Target: arm-linux-gnueabihf 2023-09-12T10:54:50,535 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:50,536 Thread model: posix 2023-09-12T10:54:50,536 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:50,537 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:50,537 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/filters.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:54:50,538 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/filters.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/descriptors/ -dumpbase filters.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccZ4x7Bj.s 2023-09-12T10:54:50,546 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:50,547 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:50,548 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:50,548 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:50,549 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:50,549 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:50,550 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:50,551 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:50,551 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:50,552 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:50,552 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:50,553 #include "..." search starts here: 2023-09-12T10:54:50,553 #include <...> search starts here: 2023-09-12T10:54:50,554 /usr/include/eigen3 2023-09-12T10:54:50,554 include 2023-09-12T10:54:50,555 /usr/include/python3.11 2023-09-12T10:54:50,556 /usr/include/c++/12 2023-09-12T10:54:50,556 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:50,557 /usr/include/c++/12/backward 2023-09-12T10:54:50,557 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:50,558 /usr/local/include 2023-09-12T10:54:50,559 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:50,559 /usr/include 2023-09-12T10:54:50,560 End of search list. 2023-09-12T10:54:50,561 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:50,561 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:50,563 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:50,564 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:50,565 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:52,206 In file included from include/openbabel/atom.h:33, 2023-09-12T10:54:52,206 from include/openbabel/mol.h:43, 2023-09-12T10:54:52,207 from ./src/descriptors/filters.cpp:21: 2023-09-12T10:54:52,208 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:52,208 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:52,209 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:52,209 | ^ 2023-09-12T10:54:52,210 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,210 37 | # define UNUSED(x) x 2023-09-12T10:54:52,211 | ^ 2023-09-12T10:54:52,898 In file included from include/openbabel/mol.h:52: 2023-09-12T10:54:52,898 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:52,899 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:52,899 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:52,900 | ^ 2023-09-12T10:54:52,901 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:52,902 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:52,902 | ^~~~~~~~ 2023-09-12T10:54:52,903 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:52,904 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:52,905 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:52,906 | ^ 2023-09-12T10:54:52,906 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:52,907 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:52,908 | ^~~~~~~~ 2023-09-12T10:54:52,922 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:52,923 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:52,924 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:52,924 | ^ 2023-09-12T10:54:52,925 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:52,926 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:52,927 | ^~~~~~~~ 2023-09-12T10:54:52,929 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:52,929 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:52,930 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:52,930 | ^ 2023-09-12T10:54:52,931 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:52,932 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:52,932 | ^~~~~~~~ 2023-09-12T10:54:53,102 In file included from include/openbabel/format.h:22, 2023-09-12T10:54:53,103 from include/openbabel/obconversion.h:37, 2023-09-12T10:54:53,103 from ./src/descriptors/filters.cpp:22: 2023-09-12T10:54:53,104 include/openbabel/plugin.h: At global scope: 2023-09-12T10:54:53,104 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:53,105 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:53,105 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:53,106 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:54:53,107 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:54:53,107 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:54:53,108 from /usr/include/c++/12/ios:42, 2023-09-12T10:54:53,108 from /usr/include/c++/12/istream:38, 2023-09-12T10:54:53,109 from /usr/include/c++/12/sstream:38, 2023-09-12T10:54:53,109 from include/openbabel/oberror.h:26, 2023-09-12T10:54:53,110 from ./src/descriptors/filters.cpp:20: 2023-09-12T10:54:53,111 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:53,111 131 | struct binary_function 2023-09-12T10:54:53,112 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:53,302 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::MWFilter::Predict(OpenBabel::OBBase*, std::string*)’: 2023-09-12T10:54:53,302 ./src/descriptors/filters.cpp:36:47: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:54:53,303 36 | virtual double Predict(OBBase* pOb, string* param=NULL) 2023-09-12T10:54:53,304 | ^ 2023-09-12T10:54:53,312 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::FormulaDescriptor::GetStringValue(OpenBabel::OBBase*, std::string&, std::string*)’: 2023-09-12T10:54:53,312 ./src/descriptors/filters.cpp:142:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:54:53,313 142 | virtual double GetStringValue(OBBase* pOb, std::string& svalue, std::string* param=NULL) 2023-09-12T10:54:53,314 | ^ 2023-09-12T10:54:55,689 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/filters.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:54:55,690 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/descriptors/filters.o /tmp/ccZ4x7Bj.s 2023-09-12T10:54:55,695 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:55,832 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:54:55,832 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:54:55,833 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/filters.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/filters.' 2023-09-12T10:54:55,833 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/descriptors/groupcontrib.cpp -o build/temp.linux-armv7l-cpython-311/./src/descriptors/groupcontrib.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:54:55,837 Using built-in specs. 2023-09-12T10:54:55,838 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:55,839 Target: arm-linux-gnueabihf 2023-09-12T10:54:55,839 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:54:55,840 Thread model: posix 2023-09-12T10:54:55,840 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:55,841 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:55,841 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/groupcontrib.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:54:55,842 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/groupcontrib.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/descriptors/ -dumpbase groupcontrib.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccZ4HDRK.s 2023-09-12T10:54:55,851 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:55,851 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:55,852 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:55,853 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:55,853 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:55,853 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:55,854 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:55,854 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:55,855 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:55,855 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:55,856 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:55,856 #include "..." search starts here: 2023-09-12T10:54:55,857 #include <...> search starts here: 2023-09-12T10:54:55,857 /usr/include/eigen3 2023-09-12T10:54:55,858 include 2023-09-12T10:54:55,858 /usr/include/python3.11 2023-09-12T10:54:55,858 /usr/include/c++/12 2023-09-12T10:54:55,859 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:55,859 /usr/include/c++/12/backward 2023-09-12T10:54:55,860 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:55,861 /usr/local/include 2023-09-12T10:54:55,861 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:55,862 /usr/include 2023-09-12T10:54:55,862 End of search list. 2023-09-12T10:54:55,863 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:55,864 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:55,865 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:55,865 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:55,868 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:57,435 In file included from include/openbabel/atom.h:33, 2023-09-12T10:54:57,435 from include/openbabel/mol.h:43, 2023-09-12T10:54:57,436 from ./src/descriptors/groupcontrib.cpp:27: 2023-09-12T10:54:57,436 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:57,437 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:57,438 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:57,438 | ^ 2023-09-12T10:54:57,439 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:57,440 37 | # define UNUSED(x) x 2023-09-12T10:54:57,440 | ^ 2023-09-12T10:54:58,203 In file included from include/openbabel/mol.h:52: 2023-09-12T10:54:58,203 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:58,204 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:58,205 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:58,205 | ^ 2023-09-12T10:54:58,206 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:58,206 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:58,207 | ^~~~~~~~ 2023-09-12T10:54:58,208 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:58,208 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:58,209 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:58,210 | ^ 2023-09-12T10:54:58,210 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:58,211 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:58,211 | ^~~~~~~~ 2023-09-12T10:54:58,227 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:58,228 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:58,228 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:58,229 | ^ 2023-09-12T10:54:58,230 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:58,230 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:58,231 | ^~~~~~~~ 2023-09-12T10:54:58,233 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:58,234 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:58,235 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:58,235 | ^ 2023-09-12T10:54:58,236 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:58,237 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:58,238 | ^~~~~~~~ 2023-09-12T10:54:58,447 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:54:58,447 from include/openbabel/groupcontrib.h:28, 2023-09-12T10:54:58,448 from ./src/descriptors/groupcontrib.cpp:29: 2023-09-12T10:54:58,449 include/openbabel/plugin.h: At global scope: 2023-09-12T10:54:58,450 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:58,451 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:58,451 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:58,452 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:54:58,452 from /usr/include/c++/12/vector:66, 2023-09-12T10:54:58,453 from ./src/descriptors/groupcontrib.cpp:25: 2023-09-12T10:54:58,454 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:58,454 131 | struct binary_function 2023-09-12T10:54:58,455 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:58,688 ./src/descriptors/groupcontrib.cpp: In member function ‘virtual double OpenBabel::OBGroupContrib::Predict(OpenBabel::OBBase*, std::string*)’: 2023-09-12T10:54:58,689 ./src/descriptors/groupcontrib.cpp:106:55: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:54:58,689 106 | double OBGroupContrib::Predict(OBBase* pOb, string* param) 2023-09-12T10:54:58,690 | ~~~~~~~~^~~~~ 2023-09-12T10:55:01,387 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:55:01,387 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: 2023-09-12T10:55:01,388 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:55:01,389 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:55:01,389 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:01,532 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:55:01,533 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:55:01,534 inlined from ‘bool OpenBabel::OBGroupContrib::ParseFile()’ at ./src/descriptors/groupcontrib.cpp:83:35: 2023-09-12T10:55:01,535 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:55:01,535 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:01,536 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:01,537 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:55:01,538 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:55:01,538 inlined from ‘bool OpenBabel::OBGroupContrib::ParseFile()’ at ./src/descriptors/groupcontrib.cpp:85:38: 2023-09-12T10:55:01,539 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2023-09-12T10:55:01,540 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:01,541 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:02,918 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/groupcontrib.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:55:02,919 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/descriptors/groupcontrib.o /tmp/ccZ4HDRK.s 2023-09-12T10:55:02,924 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:03,215 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:03,216 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:03,216 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/groupcontrib.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/groupcontrib.' 2023-09-12T10:55:03,218 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/descriptors/smartsdescriptors.cpp -o build/temp.linux-armv7l-cpython-311/./src/descriptors/smartsdescriptors.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:03,222 Using built-in specs. 2023-09-12T10:55:03,222 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:03,223 Target: arm-linux-gnueabihf 2023-09-12T10:55:03,223 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:03,224 Thread model: posix 2023-09-12T10:55:03,225 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:03,225 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:03,226 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/smartsdescriptors.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:55:03,226 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/smartsdescriptors.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/descriptors/ -dumpbase smartsdescriptors.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccVvaK8P.s 2023-09-12T10:55:03,236 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:03,236 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:03,237 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:03,238 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:03,239 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:03,239 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:03,240 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:03,240 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:03,241 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:03,242 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:03,242 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:03,243 #include "..." search starts here: 2023-09-12T10:55:03,244 #include <...> search starts here: 2023-09-12T10:55:03,244 /usr/include/eigen3 2023-09-12T10:55:03,245 include 2023-09-12T10:55:03,245 /usr/include/python3.11 2023-09-12T10:55:03,246 /usr/include/c++/12 2023-09-12T10:55:03,246 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:03,247 /usr/include/c++/12/backward 2023-09-12T10:55:03,247 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:03,248 /usr/local/include 2023-09-12T10:55:03,248 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:03,249 /usr/include 2023-09-12T10:55:03,249 End of search list. 2023-09-12T10:55:03,250 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:03,250 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:03,252 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:03,252 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:03,261 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:04,890 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:04,891 from include/openbabel/mol.h:43, 2023-09-12T10:55:04,892 from ./src/descriptors/smartsdescriptors.cpp:21: 2023-09-12T10:55:04,893 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:04,894 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:04,894 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:04,895 | ^ 2023-09-12T10:55:04,895 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:04,896 37 | # define UNUSED(x) x 2023-09-12T10:55:04,896 | ^ 2023-09-12T10:55:05,582 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:05,582 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:05,583 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:05,584 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:05,584 | ^ 2023-09-12T10:55:05,585 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:05,585 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:05,586 | ^~~~~~~~ 2023-09-12T10:55:05,590 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:05,590 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:05,591 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:05,592 | ^ 2023-09-12T10:55:05,593 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:05,593 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:05,594 | ^~~~~~~~ 2023-09-12T10:55:05,611 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:05,612 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:05,613 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:05,613 | ^ 2023-09-12T10:55:05,614 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:05,615 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:05,615 | ^~~~~~~~ 2023-09-12T10:55:05,620 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:05,621 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:05,621 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:05,622 | ^ 2023-09-12T10:55:05,623 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:05,624 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:05,624 | ^~~~~~~~ 2023-09-12T10:55:05,835 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:55:05,835 from ./src/descriptors/smartsdescriptors.cpp:22: 2023-09-12T10:55:05,836 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:05,836 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:05,837 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:05,837 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:05,838 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:55:05,838 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:55:05,839 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:55:05,840 from /usr/include/c++/12/ios:42, 2023-09-12T10:55:05,840 from /usr/include/c++/12/istream:38, 2023-09-12T10:55:05,841 from /usr/include/c++/12/sstream:38, 2023-09-12T10:55:05,841 from include/openbabel/oberror.h:26, 2023-09-12T10:55:05,842 from ./src/descriptors/smartsdescriptors.cpp:20: 2023-09-12T10:55:05,842 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:05,843 131 | struct binary_function 2023-09-12T10:55:05,843 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:05,886 ./src/descriptors/smartsdescriptors.cpp: In member function ‘virtual double OpenBabel::SmartsDescriptor::Predict(OpenBabel::OBBase*, std::string*)’: 2023-09-12T10:55:05,886 ./src/descriptors/smartsdescriptors.cpp:48:41: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:55:05,887 48 | double Predict(OBBase* pOb, string* param=NULL) 2023-09-12T10:55:05,888 | ^ 2023-09-12T10:55:07,993 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/smartsdescriptors.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/' 2023-09-12T10:55:07,993 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/descriptors/smartsdescriptors.o /tmp/ccVvaK8P.s 2023-09-12T10:55:07,998 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:08,103 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:08,104 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:08,105 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/smartsdescriptors.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/descriptors/smartsdescriptors.' 2023-09-12T10:55:08,106 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/distgeom.cpp -o build/temp.linux-armv7l-cpython-311/./src/distgeom.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:08,109 Using built-in specs. 2023-09-12T10:55:08,110 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:08,110 Target: arm-linux-gnueabihf 2023-09-12T10:55:08,111 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:08,111 Thread model: posix 2023-09-12T10:55:08,112 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:08,112 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:08,113 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/distgeom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:55:08,113 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/distgeom.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase distgeom.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccJ5q8Td.s 2023-09-12T10:55:08,122 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:08,123 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:08,124 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:08,125 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:08,125 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:08,126 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:08,127 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:08,127 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:08,128 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:08,128 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:08,129 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:08,129 #include "..." search starts here: 2023-09-12T10:55:08,130 #include <...> search starts here: 2023-09-12T10:55:08,130 /usr/include/eigen3 2023-09-12T10:55:08,130 include 2023-09-12T10:55:08,131 /usr/include/python3.11 2023-09-12T10:55:08,131 /usr/include/c++/12 2023-09-12T10:55:08,132 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:08,132 /usr/include/c++/12/backward 2023-09-12T10:55:08,132 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:08,133 /usr/local/include 2023-09-12T10:55:08,133 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:08,134 /usr/include 2023-09-12T10:55:08,134 End of search list. 2023-09-12T10:55:08,135 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:08,135 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:08,136 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:08,136 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:08,144 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:08,678 ./src/distgeom.cpp:37: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2023-09-12T10:55:08,678 37 | #pragma warning(disable : 4244) // warning C4244: '=' : conversion from 'double' to 'float', possible loss of data 2023-09-12T10:55:08,679 | 2023-09-12T10:55:08,680 ./src/distgeom.cpp:38: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2023-09-12T10:55:08,681 38 | #pragma warning(disable : 4305) // warning C4305: '*=' : truncation from 'double' to 'float' 2023-09-12T10:55:08,682 | 2023-09-12T10:55:08,683 ./src/distgeom.cpp:524:3: warning: multi-line comment [-Wcomment] 2023-09-12T10:55:08,684 524 | // \ 2023-09-12T10:55:08,684 | ^ 2023-09-12T10:55:08,685 ./src/distgeom.cpp:881:9: warning: multi-line comment [-Wcomment] 2023-09-12T10:55:08,686 881 | // / \ 2023-09-12T10:55:08,687 | ^ 2023-09-12T10:55:09,925 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:09,926 from include/openbabel/mol.h:43, 2023-09-12T10:55:09,926 from include/openbabel/distgeom.h:24, 2023-09-12T10:55:09,927 from ./src/distgeom.cpp:20: 2023-09-12T10:55:09,928 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:09,928 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:09,929 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:09,930 | ^ 2023-09-12T10:55:09,930 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:09,931 37 | # define UNUSED(x) x 2023-09-12T10:55:09,932 | ^ 2023-09-12T10:55:10,696 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:10,697 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:10,698 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:10,700 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:10,701 | ^ 2023-09-12T10:55:10,703 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:10,704 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:10,705 | ^~~~~~~~ 2023-09-12T10:55:10,707 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:10,708 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:10,709 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:10,710 | ^ 2023-09-12T10:55:10,712 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:10,713 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:10,714 | ^~~~~~~~ 2023-09-12T10:55:10,723 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:10,724 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:10,726 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:10,727 | ^ 2023-09-12T10:55:10,728 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:10,730 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:10,731 | ^~~~~~~~ 2023-09-12T10:55:10,732 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:10,734 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:10,735 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:10,736 | ^ 2023-09-12T10:55:10,738 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:10,740 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:10,741 | ^~~~~~~~ 2023-09-12T10:55:12,632 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set14Bounds()’: 2023-09-12T10:55:12,632 ./src/distgeom.cpp:479:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,633 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:55:12,634 ./src/distgeom.cpp:479:59: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,635 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:55:12,636 ./src/distgeom.cpp:486:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,636 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:55:12,637 ./src/distgeom.cpp:486:59: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,637 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:55:12,638 ./src/distgeom.cpp:500:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,639 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:55:12,639 ./src/distgeom.cpp:500:59: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,640 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:55:12,640 ./src/distgeom.cpp:506:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,641 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:55:12,642 ./src/distgeom.cpp:506:59: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:12,642 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:55:12,643 ./src/distgeom.cpp:386:18: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-12T10:55:12,643 386 | unsigned int i, j; 2023-09-12T10:55:12,644 | ^ 2023-09-12T10:55:12,645 ./src/distgeom.cpp:386:21: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-12T10:55:12,646 386 | unsigned int i, j; 2023-09-12T10:55:12,646 | ^ 2023-09-12T10:55:12,647 ./src/distgeom.cpp:426:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2023-09-12T10:55:12,648 426 | OBStereo::Ref bond_id; 2023-09-12T10:55:12,649 | ^~~~~~~ 2023-09-12T10:55:12,650 ./src/distgeom.cpp: In member function ‘OpenBabel::OBCisTransStereo* OpenBabel::OBDistanceGeometry::GetCisTransStereo(OpenBabel::OBBond*)’: 2023-09-12T10:55:12,651 ./src/distgeom.cpp:584:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2023-09-12T10:55:12,652 584 | OBStereo::Ref bond_id; 2023-09-12T10:55:12,652 | ^~~~~~~ 2023-09-12T10:55:12,661 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set15Bounds()’: 2023-09-12T10:55:12,662 ./src/distgeom.cpp:614:18: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-12T10:55:12,662 614 | unsigned int i, j; 2023-09-12T10:55:12,663 | ^ 2023-09-12T10:55:12,664 ./src/distgeom.cpp:614:21: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-12T10:55:12,665 614 | unsigned int i, j; 2023-09-12T10:55:12,665 | ^ 2023-09-12T10:55:12,672 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::TriangleSmooth(int)’: 2023-09-12T10:55:12,672 ./src/distgeom.cpp:745:9: warning: unused variable ‘loopCount’ [-Wunused-variable] 2023-09-12T10:55:12,673 745 | int loopCount = 0; 2023-09-12T10:55:12,674 | ^~~~~~~~~ 2023-09-12T10:55:12,674 ./src/distgeom.cpp:742:47: warning: unused parameter ‘iterations’ [-Wunused-parameter] 2023-09-12T10:55:12,675 742 | void OBDistanceGeometry::TriangleSmooth(int iterations) 2023-09-12T10:55:12,676 | ~~~~^~~~~~~~~~ 2023-09-12T10:55:12,745 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::AddConformer()’: 2023-09-12T10:55:12,746 ./src/distgeom.cpp:1105:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:12,746 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2023-09-12T10:55:12,747 | ~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T10:55:12,747 ./src/distgeom.cpp:1105:52: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:12,748 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2023-09-12T10:55:12,749 | ~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T10:55:12,749 ./src/distgeom.cpp:1105:77: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:12,750 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2023-09-12T10:55:12,750 | ~~~~~~~~~~~~^~~~~~~~ 2023-09-12T10:55:12,752 ./src/distgeom.cpp:1039:18: warning: unused variable ‘attempts’ [-Wunused-variable] 2023-09-12T10:55:12,753 1039 | unsigned int attempts = 0; 2023-09-12T10:55:12,754 | ^~~~~~~~ 2023-09-12T10:55:23,387 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/distgeom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:55:23,388 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/distgeom.o /tmp/ccJ5q8Td.s 2023-09-12T10:55:23,396 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:24,375 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:24,376 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:24,376 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/distgeom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/distgeom.' 2023-09-12T10:55:24,380 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/doxygen_pages.cpp -o build/temp.linux-armv7l-cpython-311/./src/doxygen_pages.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:24,385 Using built-in specs. 2023-09-12T10:55:24,386 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:24,386 Target: arm-linux-gnueabihf 2023-09-12T10:55:24,387 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:24,387 Thread model: posix 2023-09-12T10:55:24,388 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:24,389 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:24,389 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/doxygen_pages.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:55:24,390 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/doxygen_pages.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase doxygen_pages.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccu8pihU.s 2023-09-12T10:55:24,398 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:24,399 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:24,400 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:24,400 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:24,401 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:24,401 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:24,402 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:24,402 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:24,403 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:24,404 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:24,404 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:24,405 #include "..." search starts here: 2023-09-12T10:55:24,406 #include <...> search starts here: 2023-09-12T10:55:24,406 /usr/include/eigen3 2023-09-12T10:55:24,406 include 2023-09-12T10:55:24,407 /usr/include/python3.11 2023-09-12T10:55:24,407 /usr/include/c++/12 2023-09-12T10:55:24,408 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:24,408 /usr/include/c++/12/backward 2023-09-12T10:55:24,409 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:24,409 /usr/local/include 2023-09-12T10:55:24,409 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:24,410 /usr/include 2023-09-12T10:55:24,410 End of search list. 2023-09-12T10:55:24,411 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:24,411 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:24,412 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:24,413 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:24,419 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:24,438 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/doxygen_pages.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:55:24,439 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/doxygen_pages.o /tmp/ccu8pihU.s 2023-09-12T10:55:24,443 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:24,447 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:24,447 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:24,448 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/doxygen_pages.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/doxygen_pages.' 2023-09-12T10:55:24,449 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/fingerprint.cpp -o build/temp.linux-armv7l-cpython-311/./src/fingerprint.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:24,452 Using built-in specs. 2023-09-12T10:55:24,453 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:24,454 Target: arm-linux-gnueabihf 2023-09-12T10:55:24,454 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:24,455 Thread model: posix 2023-09-12T10:55:24,456 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:24,456 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:24,457 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprint.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:55:24,457 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprint.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase fingerprint.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccDfBVft.s 2023-09-12T10:55:24,466 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:24,466 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:24,467 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:24,468 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:24,469 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:24,469 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:24,470 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:24,471 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:24,471 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:24,472 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:24,472 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:24,473 #include "..." search starts here: 2023-09-12T10:55:24,473 #include <...> search starts here: 2023-09-12T10:55:24,474 /usr/include/eigen3 2023-09-12T10:55:24,474 include 2023-09-12T10:55:24,475 /usr/include/python3.11 2023-09-12T10:55:24,476 /usr/include/c++/12 2023-09-12T10:55:24,476 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:24,477 /usr/include/c++/12/backward 2023-09-12T10:55:24,477 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:24,478 /usr/local/include 2023-09-12T10:55:24,479 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:24,479 /usr/include 2023-09-12T10:55:24,480 End of search list. 2023-09-12T10:55:24,481 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:24,481 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:24,482 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:24,482 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:24,484 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:25,994 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:55:25,994 from ./src/fingerprint.cpp:27: 2023-09-12T10:55:25,995 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:25,996 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:25,996 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:25,997 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:25,997 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:25,998 from ./src/fingerprint.cpp:21: 2023-09-12T10:55:25,999 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:25,999 131 | struct binary_function 2023-09-12T10:55:26,000 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:26,148 ./src/fingerprint.cpp: In member function ‘bool OpenBabel::FastSearch::Find(OpenBabel::OBBase*, std::vector&, unsigned int)’: 2023-09-12T10:55:26,149 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2023-09-12T10:55:26,150 161 | if ( (a=((*ppat) & (*p++)) ^ (*ppat++)) ) break; 2023-09-12T10:55:26,150 | ~~~~^~ 2023-09-12T10:55:26,151 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2023-09-12T10:55:29,017 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprint.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:55:29,017 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/fingerprint.o /tmp/ccDfBVft.s 2023-09-12T10:55:29,022 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:29,249 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:29,250 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:29,250 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprint.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprint.' 2023-09-12T10:55:29,251 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/fingerprints/finger2.cpp -o build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger2.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:29,256 Using built-in specs. 2023-09-12T10:55:29,257 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:29,257 Target: arm-linux-gnueabihf 2023-09-12T10:55:29,258 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:29,258 Thread model: posix 2023-09-12T10:55:29,259 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:29,260 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:29,260 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/' 2023-09-12T10:55:29,261 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprints/finger2.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/fingerprints/ -dumpbase finger2.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccFN69op.s 2023-09-12T10:55:29,270 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:29,270 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:29,271 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:29,272 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:29,273 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:29,273 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:29,274 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:29,275 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:29,275 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:29,276 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:29,277 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:29,277 #include "..." search starts here: 2023-09-12T10:55:29,277 #include <...> search starts here: 2023-09-12T10:55:29,278 /usr/include/eigen3 2023-09-12T10:55:29,278 include 2023-09-12T10:55:29,279 /usr/include/python3.11 2023-09-12T10:55:29,279 /usr/include/c++/12 2023-09-12T10:55:29,280 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:29,280 /usr/include/c++/12/backward 2023-09-12T10:55:29,281 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:29,281 /usr/local/include 2023-09-12T10:55:29,282 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:29,282 /usr/include 2023-09-12T10:55:29,282 End of search list. 2023-09-12T10:55:29,283 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:29,284 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:29,284 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:29,285 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:29,288 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:30,874 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:30,875 from include/openbabel/mol.h:43, 2023-09-12T10:55:30,876 from ./src/fingerprints/finger2.cpp:20: 2023-09-12T10:55:30,876 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:30,877 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:30,877 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:30,878 | ^ 2023-09-12T10:55:30,878 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:30,879 37 | # define UNUSED(x) x 2023-09-12T10:55:30,880 | ^ 2023-09-12T10:55:31,643 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:31,643 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:31,644 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:31,645 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:31,646 | ^ 2023-09-12T10:55:31,646 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:31,647 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:31,648 | ^~~~~~~~ 2023-09-12T10:55:31,648 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:31,649 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:31,650 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:31,651 | ^ 2023-09-12T10:55:31,651 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:31,652 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:31,653 | ^~~~~~~~ 2023-09-12T10:55:31,667 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:31,668 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:31,668 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:31,669 | ^ 2023-09-12T10:55:31,670 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:31,670 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:31,671 | ^~~~~~~~ 2023-09-12T10:55:31,674 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:31,674 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:31,675 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:31,675 | ^ 2023-09-12T10:55:31,676 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:31,677 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:31,677 | ^~~~~~~~ 2023-09-12T10:55:31,866 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:55:31,867 from ./src/fingerprints/finger2.cpp:21: 2023-09-12T10:55:31,868 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:31,869 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:31,869 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:31,870 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:31,871 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:31,872 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:31,872 from include/openbabel/mol.h:35: 2023-09-12T10:55:31,873 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:31,874 131 | struct binary_function 2023-09-12T10:55:31,874 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:31,941 ./src/fingerprints/finger2.cpp: In member function ‘virtual std::string OpenBabel::fingerprint2::DescribeBits(std::vector, bool)’: 2023-09-12T10:55:31,941 ./src/fingerprints/finger2.cpp:63:68: warning: unused parameter ‘fp’ [-Wunused-parameter] 2023-09-12T10:55:31,942 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:55:31,943 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2023-09-12T10:55:31,944 ./src/fingerprints/finger2.cpp:63:77: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2023-09-12T10:55:31,944 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:55:31,945 | ~~~~~^~~~~~~~~ 2023-09-12T10:55:36,473 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/' 2023-09-12T10:55:36,474 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger2.o /tmp/ccFN69op.s 2023-09-12T10:55:36,478 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:36,797 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:36,798 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:36,798 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger2.' 2023-09-12T10:55:36,800 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/fingerprints/finger3.cpp -o build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger3.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:36,804 Using built-in specs. 2023-09-12T10:55:36,805 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:36,806 Target: arm-linux-gnueabihf 2023-09-12T10:55:36,806 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:36,807 Thread model: posix 2023-09-12T10:55:36,808 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:36,808 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:36,809 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger3.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/' 2023-09-12T10:55:36,809 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprints/finger3.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/fingerprints/ -dumpbase finger3.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccKRD3qa.s 2023-09-12T10:55:36,818 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:36,819 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:36,820 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:36,820 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:36,821 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:36,821 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:36,822 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:36,822 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:36,823 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:36,824 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:36,824 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:36,825 #include "..." search starts here: 2023-09-12T10:55:36,825 #include <...> search starts here: 2023-09-12T10:55:36,826 /usr/include/eigen3 2023-09-12T10:55:36,826 include 2023-09-12T10:55:36,827 /usr/include/python3.11 2023-09-12T10:55:36,828 /usr/include/c++/12 2023-09-12T10:55:36,828 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:36,829 /usr/include/c++/12/backward 2023-09-12T10:55:36,830 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:36,830 /usr/local/include 2023-09-12T10:55:36,831 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:36,831 /usr/include 2023-09-12T10:55:36,832 End of search list. 2023-09-12T10:55:36,833 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:36,833 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:36,834 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:36,835 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:36,836 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:38,390 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:38,391 from include/openbabel/mol.h:43, 2023-09-12T10:55:38,392 from ./src/fingerprints/finger3.cpp:19: 2023-09-12T10:55:38,392 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:38,393 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:38,394 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:38,395 | ^ 2023-09-12T10:55:38,396 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:38,396 37 | # define UNUSED(x) x 2023-09-12T10:55:38,397 | ^ 2023-09-12T10:55:39,160 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:39,160 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:39,161 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:39,161 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:39,162 | ^ 2023-09-12T10:55:39,162 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:39,163 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:39,164 | ^~~~~~~~ 2023-09-12T10:55:39,165 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:39,165 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:39,166 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:39,167 | ^ 2023-09-12T10:55:39,168 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:39,168 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:39,169 | ^~~~~~~~ 2023-09-12T10:55:39,184 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:39,185 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:39,185 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:39,186 | ^ 2023-09-12T10:55:39,187 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:39,188 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:39,188 | ^~~~~~~~ 2023-09-12T10:55:39,190 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:39,191 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:39,192 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:39,192 | ^ 2023-09-12T10:55:39,193 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:39,194 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:39,195 | ^~~~~~~~ 2023-09-12T10:55:39,384 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:55:39,384 from ./src/fingerprints/finger3.cpp:26: 2023-09-12T10:55:39,385 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:39,385 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:39,386 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:39,387 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:39,387 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:39,388 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:39,388 from include/openbabel/mol.h:35: 2023-09-12T10:55:39,389 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:39,389 131 | struct binary_function 2023-09-12T10:55:39,390 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:39,454 ./src/fingerprints/finger3.cpp: In member function ‘virtual bool OpenBabel::PatternFP::GetFingerprint(OpenBabel::OBBase*, std::vector&, int)’: 2023-09-12T10:55:39,455 ./src/fingerprints/finger3.cpp:108:13: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:39,455 108 | while(n < _bitcount) 2023-09-12T10:55:39,456 | ~~^~~~~~~~~~~ 2023-09-12T10:55:39,474 ./src/fingerprints/finger3.cpp: In member function ‘virtual std::string OpenBabel::PatternFP::DescribeBits(std::vector, bool)’: 2023-09-12T10:55:39,475 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2023-09-12T10:55:39,476 257 | ngrp = (num + div -1)/div--; //rounds up 2023-09-12T10:55:39,476 | ~~~^~ 2023-09-12T10:55:39,477 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2023-09-12T10:55:44,690 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger3.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/' 2023-09-12T10:55:44,691 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger3.o /tmp/ccKRD3qa.s 2023-09-12T10:55:44,700 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:45,156 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:45,158 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:45,159 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger3.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/finger3.' 2023-09-12T10:55:45,160 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/fingerprints/fingerecfp.cpp -o build/temp.linux-armv7l-cpython-311/./src/fingerprints/fingerecfp.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:45,165 Using built-in specs. 2023-09-12T10:55:45,166 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:45,166 Target: arm-linux-gnueabihf 2023-09-12T10:55:45,167 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:45,167 Thread model: posix 2023-09-12T10:55:45,168 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:45,168 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:45,169 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/fingerecfp.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/' 2023-09-12T10:55:45,170 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprints/fingerecfp.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/fingerprints/ -dumpbase fingerecfp.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc7re3KO.s 2023-09-12T10:55:45,179 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:45,179 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:45,180 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:45,181 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:45,182 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:45,183 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:45,183 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:45,184 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:45,186 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:45,186 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:45,187 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:45,187 #include "..." search starts here: 2023-09-12T10:55:45,188 #include <...> search starts here: 2023-09-12T10:55:45,188 /usr/include/eigen3 2023-09-12T10:55:45,189 include 2023-09-12T10:55:45,189 /usr/include/python3.11 2023-09-12T10:55:45,190 /usr/include/c++/12 2023-09-12T10:55:45,190 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:45,191 /usr/include/c++/12/backward 2023-09-12T10:55:45,191 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:45,192 /usr/local/include 2023-09-12T10:55:45,192 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:45,192 /usr/include 2023-09-12T10:55:45,193 End of search list. 2023-09-12T10:55:45,194 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:45,194 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:45,195 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:45,196 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:45,197 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:46,766 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:46,767 from include/openbabel/mol.h:43, 2023-09-12T10:55:46,768 from ./src/fingerprints/fingerecfp.cpp:15: 2023-09-12T10:55:46,769 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:46,769 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:46,770 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:46,771 | ^ 2023-09-12T10:55:46,771 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:46,772 37 | # define UNUSED(x) x 2023-09-12T10:55:46,773 | ^ 2023-09-12T10:55:47,535 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:47,535 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:47,536 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:47,537 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:47,537 | ^ 2023-09-12T10:55:47,538 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:47,539 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:47,539 | ^~~~~~~~ 2023-09-12T10:55:47,540 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:47,541 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:47,541 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:47,542 | ^ 2023-09-12T10:55:47,543 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:47,544 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:47,544 | ^~~~~~~~ 2023-09-12T10:55:47,559 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:47,560 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:47,560 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:47,561 | ^ 2023-09-12T10:55:47,562 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:47,562 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:47,563 | ^~~~~~~~ 2023-09-12T10:55:47,565 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:47,566 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:47,567 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:47,567 | ^ 2023-09-12T10:55:47,568 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:47,569 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:47,569 | ^~~~~~~~ 2023-09-12T10:55:47,758 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:55:47,759 from ./src/fingerprints/fingerecfp.cpp:16: 2023-09-12T10:55:47,760 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:47,760 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:47,761 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:47,761 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:47,762 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:47,763 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:47,763 from include/openbabel/mol.h:35: 2023-09-12T10:55:47,764 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:47,765 131 | struct binary_function 2023-09-12T10:55:47,765 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:47,811 ./src/fingerprints/fingerecfp.cpp: In member function ‘virtual std::string OpenBabel::fingerprintECFP::DescribeBits(std::vector, bool)’: 2023-09-12T10:55:47,812 ./src/fingerprints/fingerecfp.cpp:43:70: warning: unused parameter ‘fp’ [-Wunused-parameter] 2023-09-12T10:55:47,812 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:55:47,813 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2023-09-12T10:55:47,814 ./src/fingerprints/fingerecfp.cpp:43:79: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2023-09-12T10:55:47,814 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:55:47,815 | ~~~~~^~~~~~~~~ 2023-09-12T10:55:49,113 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(unsigned char*, unsigned int)’: 2023-09-12T10:55:49,114 ./src/fingerprints/fingerecfp.cpp:105:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,114 105 | case 11: c += ((unsigned int)ptr[10]<<24); 2023-09-12T10:55:49,115 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,115 ./src/fingerprints/fingerecfp.cpp:106:3: note: here 2023-09-12T10:55:49,116 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2023-09-12T10:55:49,116 | ^~~~ 2023-09-12T10:55:49,117 ./src/fingerprints/fingerecfp.cpp:106:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,117 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2023-09-12T10:55:49,117 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,118 ./src/fingerprints/fingerecfp.cpp:107:3: note: here 2023-09-12T10:55:49,118 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2023-09-12T10:55:49,119 | ^~~~ 2023-09-12T10:55:49,120 ./src/fingerprints/fingerecfp.cpp:107:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,120 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2023-09-12T10:55:49,121 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,121 ./src/fingerprints/fingerecfp.cpp:108:3: note: here 2023-09-12T10:55:49,122 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2023-09-12T10:55:49,122 | ^~~~ 2023-09-12T10:55:49,123 ./src/fingerprints/fingerecfp.cpp:108:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,123 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2023-09-12T10:55:49,124 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,124 ./src/fingerprints/fingerecfp.cpp:109:3: note: here 2023-09-12T10:55:49,125 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2023-09-12T10:55:49,126 | ^~~~ 2023-09-12T10:55:49,126 ./src/fingerprints/fingerecfp.cpp:109:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,127 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2023-09-12T10:55:49,128 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,129 ./src/fingerprints/fingerecfp.cpp:110:3: note: here 2023-09-12T10:55:49,129 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2023-09-12T10:55:49,130 | ^~~~ 2023-09-12T10:55:49,131 ./src/fingerprints/fingerecfp.cpp:110:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,131 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2023-09-12T10:55:49,132 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,133 ./src/fingerprints/fingerecfp.cpp:111:3: note: here 2023-09-12T10:55:49,133 111 | case 5: b += ptr[4]; 2023-09-12T10:55:49,134 | ^~~~ 2023-09-12T10:55:49,135 ./src/fingerprints/fingerecfp.cpp:111:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,135 111 | case 5: b += ptr[4]; 2023-09-12T10:55:49,136 | ~~^~~~~~~~~ 2023-09-12T10:55:49,137 ./src/fingerprints/fingerecfp.cpp:112:3: note: here 2023-09-12T10:55:49,137 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2023-09-12T10:55:49,138 | ^~~~ 2023-09-12T10:55:49,139 ./src/fingerprints/fingerecfp.cpp:112:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,139 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2023-09-12T10:55:49,140 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,141 ./src/fingerprints/fingerecfp.cpp:113:3: note: here 2023-09-12T10:55:49,142 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2023-09-12T10:55:49,142 | ^~~~ 2023-09-12T10:55:49,143 ./src/fingerprints/fingerecfp.cpp:113:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,144 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2023-09-12T10:55:49,144 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,144 ./src/fingerprints/fingerecfp.cpp:114:3: note: here 2023-09-12T10:55:49,145 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2023-09-12T10:55:49,145 | ^~~~ 2023-09-12T10:55:49,146 ./src/fingerprints/fingerecfp.cpp:114:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,146 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2023-09-12T10:55:49,147 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:49,147 ./src/fingerprints/fingerecfp.cpp:115:3: note: here 2023-09-12T10:55:49,148 115 | case 1: a += ptr[0]; 2023-09-12T10:55:49,148 | ^~~~ 2023-09-12T10:55:49,149 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(std::vector&)’: 2023-09-12T10:55:49,149 ./src/fingerprints/fingerecfp.cpp:139:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:55:49,150 139 | case 2: b += v[i+1]; 2023-09-12T10:55:49,150 ./src/fingerprints/fingerecfp.cpp:140:3: note: here 2023-09-12T10:55:49,151 140 | case 1: a += v[i]; 2023-09-12T10:55:49,151 | ^~~~ 2023-09-12T10:55:51,826 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/fingerecfp.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/' 2023-09-12T10:55:51,827 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/fingerprints/fingerecfp.o /tmp/cc7re3KO.s 2023-09-12T10:55:51,831 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:52,048 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:55:52,048 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:55:52,049 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/fingerecfp.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/fingerprints/fingerecfp.' 2023-09-12T10:55:52,050 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/forcefield.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefield.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:52,054 Using built-in specs. 2023-09-12T10:55:52,055 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:52,055 Target: arm-linux-gnueabihf 2023-09-12T10:55:52,056 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:55:52,056 Thread model: posix 2023-09-12T10:55:52,056 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:52,057 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:52,057 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefield.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:55:52,058 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefield.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase forcefield.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccU6bz8c.s 2023-09-12T10:55:52,067 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:52,067 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:52,068 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:52,069 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:52,069 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:52,070 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:52,070 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:52,071 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:52,071 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:52,072 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:52,073 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:52,073 #include "..." search starts here: 2023-09-12T10:55:52,074 #include <...> search starts here: 2023-09-12T10:55:52,075 /usr/include/eigen3 2023-09-12T10:55:52,075 include 2023-09-12T10:55:52,076 /usr/include/python3.11 2023-09-12T10:55:52,076 /usr/include/c++/12 2023-09-12T10:55:52,077 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:52,078 /usr/include/c++/12/backward 2023-09-12T10:55:52,078 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:52,079 /usr/local/include 2023-09-12T10:55:52,079 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:52,079 /usr/include 2023-09-12T10:55:52,080 End of search list. 2023-09-12T10:55:52,080 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:52,081 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:52,082 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:52,082 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:52,087 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:53,645 In file included from include/openbabel/forcefield.h:30, 2023-09-12T10:55:53,646 from ./src/forcefield.cpp:22: 2023-09-12T10:55:53,646 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:53,647 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:53,647 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:53,648 | ^ 2023-09-12T10:55:53,648 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:53,649 37 | # define UNUSED(x) x 2023-09-12T10:55:53,649 | ^ 2023-09-12T10:55:54,461 In file included from include/openbabel/mol.h:52, 2023-09-12T10:55:54,462 from include/openbabel/forcefield.h:31: 2023-09-12T10:55:54,463 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:54,463 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:54,464 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:54,465 | ^ 2023-09-12T10:55:54,466 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:54,466 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:54,467 | ^~~~~~~~ 2023-09-12T10:55:54,468 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:54,469 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:54,469 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:54,470 | ^ 2023-09-12T10:55:54,471 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:54,471 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:54,472 | ^~~~~~~~ 2023-09-12T10:55:54,487 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:54,488 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:54,489 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:54,489 | ^ 2023-09-12T10:55:54,490 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:54,491 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:54,491 | ^~~~~~~~ 2023-09-12T10:55:54,494 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:54,495 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:54,495 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:54,496 | ^ 2023-09-12T10:55:54,497 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:54,498 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:54,499 | ^~~~~~~~ 2023-09-12T10:55:54,670 In file included from include/openbabel/forcefield.h:32: 2023-09-12T10:55:54,671 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:54,672 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:54,672 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:54,673 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:54,674 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:54,674 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:54,675 from include/openbabel/forcefield.h:23: 2023-09-12T10:55:54,676 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:54,677 131 | struct binary_function 2023-09-12T10:55:54,677 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:54,799 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:55:54,799 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,800 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,801 | ^ 2023-09-12T10:55:54,801 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,802 37 | # define UNUSED(x) x 2023-09-12T10:55:54,803 | ^ 2023-09-12T10:55:54,804 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:55:54,804 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,805 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,806 | ^ 2023-09-12T10:55:54,806 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,807 37 | # define UNUSED(x) x 2023-09-12T10:55:54,808 | ^ 2023-09-12T10:55:54,808 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:55:54,809 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,810 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,811 | ^ 2023-09-12T10:55:54,811 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,812 37 | # define UNUSED(x) x 2023-09-12T10:55:54,812 | ^ 2023-09-12T10:55:54,813 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:55:54,813 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,814 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,815 | ^ 2023-09-12T10:55:54,815 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,816 37 | # define UNUSED(x) x 2023-09-12T10:55:54,816 | ^ 2023-09-12T10:55:54,817 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:55:54,817 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,818 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,818 | ^ 2023-09-12T10:55:54,819 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,819 37 | # define UNUSED(x) x 2023-09-12T10:55:54,820 | ^ 2023-09-12T10:55:54,820 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:55:54,821 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,822 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,823 | ^ 2023-09-12T10:55:54,823 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,824 37 | # define UNUSED(x) x 2023-09-12T10:55:54,825 | ^ 2023-09-12T10:55:54,825 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:55:54,826 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,827 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,827 | ^ 2023-09-12T10:55:54,828 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,829 37 | # define UNUSED(x) x 2023-09-12T10:55:54,829 | ^ 2023-09-12T10:55:54,830 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:55:54,830 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:54,831 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:54,832 | ^ 2023-09-12T10:55:54,832 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,833 37 | # define UNUSED(x) x 2023-09-12T10:55:54,834 | ^ 2023-09-12T10:55:54,852 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:55:54,853 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:55:54,854 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:55:54,855 | ^ 2023-09-12T10:55:54,856 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,856 37 | # define UNUSED(x) x 2023-09-12T10:55:54,857 | ^ 2023-09-12T10:55:54,857 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:55:54,858 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:55:54,858 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:55:54,859 | ^ 2023-09-12T10:55:54,859 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:54,860 37 | # define UNUSED(x) x 2023-09-12T10:55:54,860 | ^ 2023-09-12T10:55:54,971 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int)’: 2023-09-12T10:55:54,971 ./src/forcefield.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:54,972 384 | if (_ignoreAtom == a) 2023-09-12T10:55:54,972 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:55:54,973 ./src/forcefield.cpp:386:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:54,974 386 | if (_ignoreAtom == b) 2023-09-12T10:55:54,974 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:55:54,975 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int)’: 2023-09-12T10:55:54,976 ./src/forcefield.cpp:396:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:54,977 396 | if (_ignoreAtom == b) 2023-09-12T10:55:54,977 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:55:54,978 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int, int)’: 2023-09-12T10:55:54,979 ./src/forcefield.cpp:406:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:55:54,979 406 | if (_ignoreAtom == d) 2023-09-12T10:55:54,980 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:55:55,000 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintType(int) const’: 2023-09-12T10:55:55,000 ./src/forcefield.cpp:658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,001 658 | if (index >= _constraints.size()) 2023-09-12T10:55:55,002 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:55,003 ./src/forcefield.cpp: In member function ‘double OpenBabel::OBFFConstraints::GetConstraintValue(int) const’: 2023-09-12T10:55:55,003 ./src/forcefield.cpp:666:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,004 666 | if (index >= _constraints.size()) 2023-09-12T10:55:55,005 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:55,005 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomA(int) const’: 2023-09-12T10:55:55,006 ./src/forcefield.cpp:674:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,007 674 | if (index >= _constraints.size()) 2023-09-12T10:55:55,007 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:55,008 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomB(int) const’: 2023-09-12T10:55:55,009 ./src/forcefield.cpp:682:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,010 682 | if (index >= _constraints.size()) 2023-09-12T10:55:55,011 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:55,011 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomC(int) const’: 2023-09-12T10:55:55,012 ./src/forcefield.cpp:690:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,012 690 | if (index >= _constraints.size()) 2023-09-12T10:55:55,013 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:55,013 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomD(int) const’: 2023-09-12T10:55:55,014 ./src/forcefield.cpp:698:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,015 698 | if (index >= _constraints.size()) 2023-09-12T10:55:55,015 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:55,067 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2023-09-12T10:55:55,068 ./src/forcefield.cpp:1358:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2023-09-12T10:55:55,068 1358 | num_permutations = factorial[num_rotors_to_permute]; 2023-09-12T10:55:55,069 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:55,070 ./src/forcefield.cpp:1362:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,071 1362 | for (int i=0; i::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:55:55,093 1375 | for (int i=0; i >&, std::vector, double)’: 2023-09-12T10:55:55,118 ./src/forcefield.cpp:1576:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:55,118 1576 | if (j == rotorKey[i]) 2023-09-12T10:55:55,119 ./src/forcefield.cpp:1595:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2023-09-12T10:55:55,120 1595 | if (j == rotorKey[i]) 2023-09-12T10:55:55,146 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::DistanceGeometry()’: 2023-09-12T10:55:55,146 ./src/forcefield.cpp:1975:26: warning: variable ‘l_bc’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:55:55,147 1975 | double l_ab, l_bc, l_ac; // lower limits 2023-09-12T10:55:55,148 | ^~~~ 2023-09-12T10:55:55,198 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::SteepestDescentInitialize(int, double, int)’: 2023-09-12T10:55:55,199 ./src/forcefield.cpp:2747:77: warning: unused parameter ‘method’ [-Wunused-parameter] 2023-09-12T10:55:55,199 2747 | void OBForceField::SteepestDescentInitialize(int steps, double econv, int method) 2023-09-12T10:55:55,200 | ~~~~^~~~~~ 2023-09-12T10:55:55,210 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ConjugateGradientsInitialize(int, double, int)’: 2023-09-12T10:55:55,210 ./src/forcefield.cpp:2873:55: warning: unused parameter ‘method’ [-Wunused-parameter] 2023-09-12T10:55:55,211 2873 | int method) 2023-09-12T10:55:55,211 | ~~~~^~~~~~ 2023-09-12T10:55:55,250 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::MolecularDynamicsTakeNSteps(int, double, double, int)’: 2023-09-12T10:55:55,250 ./src/forcefield.cpp:3524:88: warning: unused parameter ‘method’ [-Wunused-parameter] 2023-09-12T10:55:55,251 3524 | void OBForceField::MolecularDynamicsTakeNSteps(int n, double T, double timestep, int method) 2023-09-12T10:55:55,251 | ~~~~^~~~~~ 2023-09-12T10:56:08,699 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:56:08,699 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’: 2023-09-12T10:56:08,700 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:08,700 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:08,701 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:08,816 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,817 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,818 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,818 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,819 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2023-09-12T10:56:08,820 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,820 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,821 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,822 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2023-09-12T10:56:08,822 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,823 645 | OBFFConstraint constraint; 2023-09-12T10:56:08,824 | ^~~~~~~~~~ 2023-09-12T10:56:08,824 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,825 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,825 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,826 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,826 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2023-09-12T10:56:08,827 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,827 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,828 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,828 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2023-09-12T10:56:08,828 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,829 645 | OBFFConstraint constraint; 2023-09-12T10:56:08,829 | ^~~~~~~~~~ 2023-09-12T10:56:08,830 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:56:08,831 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:08,832 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2023-09-12T10:56:08,832 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:08,833 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:08,834 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:08,873 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,874 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,875 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,875 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,876 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2023-09-12T10:56:08,877 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,877 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,878 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,879 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2023-09-12T10:56:08,879 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,880 570 | OBFFConstraint constraint; 2023-09-12T10:56:08,880 | ^~~~~~~~~~ 2023-09-12T10:56:08,881 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,881 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,882 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,882 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,883 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2023-09-12T10:56:08,883 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,884 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,884 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,885 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2023-09-12T10:56:08,885 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,886 570 | OBFFConstraint constraint; 2023-09-12T10:56:08,886 | ^~~~~~~~~~ 2023-09-12T10:56:08,887 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:08,888 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2023-09-12T10:56:08,888 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:08,889 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:08,890 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:08,928 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,929 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,929 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,930 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,930 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2023-09-12T10:56:08,931 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,932 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,933 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,933 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2023-09-12T10:56:08,934 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,934 580 | OBFFConstraint constraint; 2023-09-12T10:56:08,934 | ^~~~~~~~~~ 2023-09-12T10:56:08,935 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,935 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,936 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,936 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,937 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2023-09-12T10:56:08,937 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,938 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,938 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,939 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2023-09-12T10:56:08,940 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,940 580 | OBFFConstraint constraint; 2023-09-12T10:56:08,941 | ^~~~~~~~~~ 2023-09-12T10:56:08,941 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:08,942 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2023-09-12T10:56:08,943 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:08,943 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:08,944 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:08,983 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,984 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,984 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,985 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,986 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2023-09-12T10:56:08,986 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,987 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,988 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,988 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2023-09-12T10:56:08,989 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,989 602 | OBFFConstraint constraint; 2023-09-12T10:56:08,990 | ^~~~~~~~~~ 2023-09-12T10:56:08,990 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:08,990 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:08,991 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:08,991 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:08,992 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2023-09-12T10:56:08,992 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:08,993 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:08,994 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:08,994 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2023-09-12T10:56:08,995 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2023-09-12T10:56:08,996 602 | OBFFConstraint constraint; 2023-09-12T10:56:08,996 | ^~~~~~~~~~ 2023-09-12T10:56:08,997 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:08,998 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2023-09-12T10:56:08,998 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:08,999 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:09,000 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:09,038 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,039 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,040 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,040 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,041 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2023-09-12T10:56:09,042 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,042 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,043 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,043 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2023-09-12T10:56:09,044 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,044 591 | OBFFConstraint constraint; 2023-09-12T10:56:09,045 | ^~~~~~~~~~ 2023-09-12T10:56:09,045 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,046 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,046 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,047 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,047 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2023-09-12T10:56:09,048 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,048 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,049 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,050 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2023-09-12T10:56:09,050 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,051 591 | OBFFConstraint constraint; 2023-09-12T10:56:09,052 | ^~~~~~~~~~ 2023-09-12T10:56:09,052 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:09,053 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2023-09-12T10:56:09,054 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:09,054 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:09,055 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:09,091 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,091 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,092 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,093 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,093 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2023-09-12T10:56:09,094 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,094 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,095 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,095 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2023-09-12T10:56:09,096 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,096 622 | OBFFConstraint constraint; 2023-09-12T10:56:09,097 | ^~~~~~~~~~ 2023-09-12T10:56:09,097 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,098 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,098 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,099 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,099 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2023-09-12T10:56:09,100 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,101 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,101 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,102 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2023-09-12T10:56:09,103 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,104 622 | OBFFConstraint constraint; 2023-09-12T10:56:09,104 | ^~~~~~~~~~ 2023-09-12T10:56:09,105 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:09,105 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2023-09-12T10:56:09,106 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:09,106 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:09,107 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:09,143 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,143 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,144 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,145 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,146 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2023-09-12T10:56:09,146 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,147 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,147 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,147 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2023-09-12T10:56:09,148 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,148 613 | OBFFConstraint constraint; 2023-09-12T10:56:09,149 | ^~~~~~~~~~ 2023-09-12T10:56:09,149 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,150 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,150 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,151 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,151 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2023-09-12T10:56:09,152 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,153 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,153 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,154 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2023-09-12T10:56:09,155 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,155 613 | OBFFConstraint constraint; 2023-09-12T10:56:09,156 | ^~~~~~~~~~ 2023-09-12T10:56:09,156 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:09,157 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2023-09-12T10:56:09,157 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:09,158 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:09,159 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:09,197 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,198 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,199 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,200 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,201 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2023-09-12T10:56:09,201 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,202 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,202 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,203 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2023-09-12T10:56:09,203 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,204 633 | OBFFConstraint constraint; 2023-09-12T10:56:09,204 | ^~~~~~~~~~ 2023-09-12T10:56:09,205 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:56:09,205 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:09,206 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:09,207 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:09,207 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2023-09-12T10:56:09,208 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,209 235 | class OBFPRT OBFFConstraint 2023-09-12T10:56:09,209 | ^~~~~~~~~~~~~~ 2023-09-12T10:56:09,210 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2023-09-12T10:56:09,211 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2023-09-12T10:56:09,211 633 | OBFFConstraint constraint; 2023-09-12T10:56:09,212 | ^~~~~~~~~~ 2023-09-12T10:56:09,212 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:56:09,213 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2023-09-12T10:56:09,214 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:09,214 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:09,215 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:09,837 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2023-09-12T10:56:09,838 ./src/forcefield.cpp:1415:11: warning: ‘minE’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,838 1415 | if (minE < best_minE) { 2023-09-12T10:56:09,839 | ^~ 2023-09-12T10:56:09,839 ./src/forcefield.cpp:1325:22: note: ‘minE’ was declared here 2023-09-12T10:56:09,840 1325 | double currentE, minE, best_minE; 2023-09-12T10:56:09,840 | ^~~~ 2023-09-12T10:56:09,841 ./src/forcefield.cpp:1398:29: warning: ‘minj’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:09,841 1398 | rotorKey[idx + 1] = minj; 2023-09-12T10:56:09,842 | ^~~~ 2023-09-12T10:56:09,843 ./src/forcefield.cpp:1324:21: note: ‘minj’ was declared here 2023-09-12T10:56:09,843 1324 | unsigned int j, minj; 2023-09-12T10:56:09,844 | ^~~~ 2023-09-12T10:56:10,601 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:56:10,602 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:10,602 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:10,603 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:11,250 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:56:11,250 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:11,312 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:56:11,312 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:11,372 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:11,420 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:11,421 inlined from ‘bool OpenBabel::OBForceField::RandomRotorSearchNextConformer(unsigned int)’ at ./src/forcefield.cpp:1540:24: 2023-09-12T10:56:11,422 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:11,422 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:11,423 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:11,453 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:11,454 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:11,454 inlined from ‘bool OpenBabel::OBForceField::SystematicRotorSearchNextConformer(unsigned int)’ at ./src/forcefield.cpp:1274:24: 2023-09-12T10:56:11,455 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:11,456 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:11,457 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:11,960 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:11,960 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:11,961 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1660:26: 2023-09-12T10:56:11,961 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:11,962 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:11,962 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:11,963 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:11,964 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:11,964 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1665:24: 2023-09-12T10:56:11,965 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:11,965 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:11,966 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:11,967 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:11,968 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1714:27: 2023-09-12T10:56:11,969 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:11,969 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:11,970 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:11,971 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:11,972 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1733:28: 2023-09-12T10:56:11,972 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:11,973 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:11,973 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:11,974 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:11,975 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1790:26: 2023-09-12T10:56:11,976 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:11,977 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:11,977 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:13,134 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:56:13,134 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:13,135 inlined from ‘bool OpenBabel::OBForceField::GetCoordinates(OpenBabel::OBMol&)’ at ./src/forcefield.cpp:1049:23: 2023-09-12T10:56:13,136 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:13,136 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:13,137 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:14,673 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefield.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:56:14,674 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/forcefield.o /tmp/ccU6bz8c.s 2023-09-12T10:56:14,679 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:16,015 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:56:16,015 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:56:16,016 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefield.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefield.' 2023-09-12T10:56:16,021 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/forcefields/forcefieldgaff.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldgaff.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:56:16,025 Using built-in specs. 2023-09-12T10:56:16,027 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:16,027 Target: arm-linux-gnueabihf 2023-09-12T10:56:16,028 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:56:16,029 Thread model: posix 2023-09-12T10:56:16,029 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:16,030 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:16,030 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldgaff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:56:16,031 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldgaff.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/forcefields/ -dumpbase forcefieldgaff.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccvaB7k6.s 2023-09-12T10:56:16,039 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:16,040 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:16,041 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:16,041 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:16,042 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:16,043 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:16,043 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:16,044 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:16,045 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:16,045 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:16,046 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:16,046 #include "..." search starts here: 2023-09-12T10:56:16,047 #include <...> search starts here: 2023-09-12T10:56:16,047 /usr/include/eigen3 2023-09-12T10:56:16,048 include 2023-09-12T10:56:16,048 /usr/include/python3.11 2023-09-12T10:56:16,049 /usr/include/c++/12 2023-09-12T10:56:16,049 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:16,050 /usr/include/c++/12/backward 2023-09-12T10:56:16,051 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:16,051 /usr/local/include 2023-09-12T10:56:16,052 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:16,053 /usr/include 2023-09-12T10:56:16,053 End of search list. 2023-09-12T10:56:16,054 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:16,055 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:16,056 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:16,056 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:16,058 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:17,696 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:17,697 from include/openbabel/mol.h:43, 2023-09-12T10:56:17,698 from ./src/forcefields/forcefieldgaff.cpp:21: 2023-09-12T10:56:17,698 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:17,699 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:17,700 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:17,700 | ^ 2023-09-12T10:56:17,701 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:17,701 37 | # define UNUSED(x) x 2023-09-12T10:56:17,702 | ^ 2023-09-12T10:56:18,470 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:18,470 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:18,471 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:18,472 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:18,473 | ^ 2023-09-12T10:56:18,473 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:18,474 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:18,475 | ^~~~~~~~ 2023-09-12T10:56:18,476 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:18,477 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:18,477 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:18,478 | ^ 2023-09-12T10:56:18,479 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:18,480 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:18,480 | ^~~~~~~~ 2023-09-12T10:56:18,494 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:18,495 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:18,496 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:18,497 | ^ 2023-09-12T10:56:18,498 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:18,499 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:18,499 | ^~~~~~~~ 2023-09-12T10:56:18,501 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:18,502 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:18,502 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:18,503 | ^ 2023-09-12T10:56:18,503 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:18,504 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:18,505 | ^~~~~~~~ 2023-09-12T10:56:18,816 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:56:18,817 from include/forcefields/forcefieldgaff.h:24, 2023-09-12T10:56:18,817 from ./src/forcefields/forcefieldgaff.cpp:24: 2023-09-12T10:56:18,818 include/openbabel/plugin.h: At global scope: 2023-09-12T10:56:18,818 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:18,819 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:18,820 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:18,820 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:56:18,821 from /usr/include/c++/12/vector:66, 2023-09-12T10:56:18,821 from include/openbabel/mol.h:35: 2023-09-12T10:56:18,822 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:18,823 131 | struct binary_function 2023-09-12T10:56:18,824 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:18,944 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:56:18,945 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,946 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,946 | ^ 2023-09-12T10:56:18,947 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,948 37 | # define UNUSED(x) x 2023-09-12T10:56:18,948 | ^ 2023-09-12T10:56:18,949 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:56:18,950 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,950 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,951 | ^ 2023-09-12T10:56:18,952 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,952 37 | # define UNUSED(x) x 2023-09-12T10:56:18,953 | ^ 2023-09-12T10:56:18,954 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:56:18,955 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,955 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,956 | ^ 2023-09-12T10:56:18,957 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,958 37 | # define UNUSED(x) x 2023-09-12T10:56:18,958 | ^ 2023-09-12T10:56:18,959 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:56:18,959 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,960 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,960 | ^ 2023-09-12T10:56:18,961 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,961 37 | # define UNUSED(x) x 2023-09-12T10:56:18,962 | ^ 2023-09-12T10:56:18,962 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:56:18,963 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,963 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,964 | ^ 2023-09-12T10:56:18,964 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,965 37 | # define UNUSED(x) x 2023-09-12T10:56:18,965 | ^ 2023-09-12T10:56:18,966 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:56:18,966 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,967 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,968 | ^ 2023-09-12T10:56:18,968 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,969 37 | # define UNUSED(x) x 2023-09-12T10:56:18,970 | ^ 2023-09-12T10:56:18,970 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:56:18,971 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,972 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,972 | ^ 2023-09-12T10:56:18,973 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,974 37 | # define UNUSED(x) x 2023-09-12T10:56:18,974 | ^ 2023-09-12T10:56:18,975 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:56:18,976 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:18,976 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:18,977 | ^ 2023-09-12T10:56:18,977 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:18,978 37 | # define UNUSED(x) x 2023-09-12T10:56:18,979 | ^ 2023-09-12T10:56:26,822 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:56:26,823 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:26,823 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:26,824 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:26,825 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:26,967 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:26,967 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:27,157 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:27,158 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:27,343 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:56:27,344 /usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:27,345 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:27,345 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:27,346 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:27,448 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:27,448 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:27,449 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:27,450 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:27,634 /usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:27,635 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:27,636 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:27,636 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:27,726 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:27,727 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:27,727 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:27,728 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:27,862 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFElectrostaticCalculationGaff&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGaff; _Alloc = std::allocator]’: 2023-09-12T10:56:27,863 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:28,721 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,721 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:56:28,722 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,723 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,723 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,724 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:56:28,724 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,725 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,725 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,726 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,727 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,727 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,728 | ^~~~~~~~ 2023-09-12T10:56:28,729 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,730 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:56:28,730 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,731 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,731 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,732 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:56:28,733 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,734 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,735 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,735 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,736 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,736 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,737 | ^~~~~~~~ 2023-09-12T10:56:28,737 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,738 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:56:28,739 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,740 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,740 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,741 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:56:28,741 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,742 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,742 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,743 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,743 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,744 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,744 | ^~~~~~~~ 2023-09-12T10:56:28,745 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:56:28,745 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,745 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,746 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,746 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:56:28,747 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,748 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:56:28,748 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,748 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,749 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,749 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,749 | ^~~~~~~~ 2023-09-12T10:56:28,750 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:56:28,750 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,750 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,751 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,751 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:56:28,751 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,752 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:56:28,752 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,753 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,753 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,754 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,754 | ^~~~~~~~ 2023-09-12T10:56:28,755 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,755 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:56:28,756 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,756 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,757 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,758 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:56:28,758 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,759 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,759 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,759 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,760 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,760 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,761 | ^~~~~~~~ 2023-09-12T10:56:28,761 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,761 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:56:28,762 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,762 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,762 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,763 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:56:28,763 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,764 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,764 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,765 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,765 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,766 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,766 | ^~~~~~~~ 2023-09-12T10:56:28,767 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,767 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:56:28,768 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,768 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,768 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,769 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:56:28,770 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,770 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,770 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,771 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,771 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,771 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,772 | ^~~~~~~~ 2023-09-12T10:56:28,772 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:56:28,772 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,773 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,773 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,774 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:56:28,774 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,775 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:56:28,775 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,776 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,776 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,777 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,777 | ^~~~~~~~ 2023-09-12T10:56:28,777 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:56:28,778 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,778 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,779 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,779 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:56:28,780 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,781 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:56:28,781 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,781 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,782 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:56:28,782 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:56:28,782 | ^~~~~~~~ 2023-09-12T10:56:28,782 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,783 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,784 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,784 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,785 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,785 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,786 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:56:28,786 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,787 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,788 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,789 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,789 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,790 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,791 | ^~~~~~~~~ 2023-09-12T10:56:28,791 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,792 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,793 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,794 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,795 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,795 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,796 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:56:28,797 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,797 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,798 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,798 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,799 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,800 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,800 | ^~~~~~~~~ 2023-09-12T10:56:28,801 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,801 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,802 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,803 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,803 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,804 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,805 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:56:28,806 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,806 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,807 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,808 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,809 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,809 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,810 | ^~~~~~~~~ 2023-09-12T10:56:28,811 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:28,812 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,812 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,813 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,814 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,814 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:56:28,815 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,815 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:28,816 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,817 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,818 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,818 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,819 | ^~~~~~~~~ 2023-09-12T10:56:28,820 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:56:28,821 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,822 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,822 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,823 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:56:28,824 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,825 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:56:28,825 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,826 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,827 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,827 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,828 | ^~~~~~~~~ 2023-09-12T10:56:28,829 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:56:28,829 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,830 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,830 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,831 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:56:28,831 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,832 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:56:28,833 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,833 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,834 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,835 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,835 | ^~~~~~~~~ 2023-09-12T10:56:28,836 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,837 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,837 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,838 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,839 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,840 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,840 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:56:28,841 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,841 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,842 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,843 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,843 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,844 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,844 | ^~~~~~~~~ 2023-09-12T10:56:28,845 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,845 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,846 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,846 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,847 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,847 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,848 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:56:28,849 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,849 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,850 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,851 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,851 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,852 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,853 | ^~~~~~~~~ 2023-09-12T10:56:28,853 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,854 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,855 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,855 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,856 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,857 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,857 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:56:28,858 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,858 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,859 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,859 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,860 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,860 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,861 | ^~~~~~~~~ 2023-09-12T10:56:28,862 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:28,862 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:56:28,863 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,864 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,865 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,866 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:56:28,866 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,867 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:28,868 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,869 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,870 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,870 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,871 | ^~~~~~~~~ 2023-09-12T10:56:28,871 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:56:28,872 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,873 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,874 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,875 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:56:28,875 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,876 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:56:28,877 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,877 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,878 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,878 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,879 | ^~~~~~~~~ 2023-09-12T10:56:28,879 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:56:28,880 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,880 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGaff; _Args = {const OpenBabel::OBFFAngleCalculationGaff&}; _Tp = OpenBabel::OBFFAngleCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,881 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,881 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:56:28,882 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,882 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:56:28,883 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,884 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,884 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:56:28,885 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:56:28,885 | ^~~~~~~~~ 2023-09-12T10:56:28,886 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,886 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,887 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,888 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:56:28,889 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,889 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,890 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,890 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:56:28,891 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,891 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,892 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,892 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,893 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:56:28,894 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:56:28,894 | ^~~~~~~~~~~ 2023-09-12T10:56:28,895 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,896 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,897 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,898 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:56:28,898 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,899 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,900 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,900 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:56:28,901 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,902 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,903 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,904 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,905 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:56:28,905 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:56:28,906 | ^~~~~~~~~~~ 2023-09-12T10:56:28,906 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,907 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,907 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,908 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:56:28,909 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,909 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,910 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,910 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:56:28,911 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,912 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,913 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,914 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,914 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:56:28,915 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:56:28,915 | ^~~~~~~~~~~ 2023-09-12T10:56:28,916 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:28,916 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,917 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:56:28,918 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,918 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,919 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,920 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:56:28,920 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,920 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:28,921 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,921 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,922 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:56:28,922 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:56:28,923 | ^~~~~~~~~~~ 2023-09-12T10:56:28,923 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:56:28,924 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:56:28,924 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,925 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,926 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,926 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:56:28,927 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,928 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:56:28,928 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,929 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,929 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:56:28,930 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:56:28,930 | ^~~~~~~~~~~ 2023-09-12T10:56:28,931 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’, 2023-09-12T10:56:28,932 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,932 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGaff; _Args = {const OpenBabel::OBFFTorsionCalculationGaff&}; _Tp = OpenBabel::OBFFTorsionCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,933 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,933 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:56:28,934 include/forcefields/forcefieldgaff.h:47:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,934 47 | class OBFFTorsionCalculationGaff : public OBFFCalculation4 2023-09-12T10:56:28,935 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,935 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,936 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:56:28,936 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:56:28,937 | ^~~~~~~~~~~ 2023-09-12T10:56:28,938 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,938 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,939 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,940 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:28,940 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,941 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,942 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,943 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:56:28,943 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,944 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,945 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,946 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,946 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:28,947 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:28,947 | ^~~~~~~ 2023-09-12T10:56:28,948 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,949 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,949 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,950 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:28,950 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,951 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,952 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,953 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:56:28,953 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,954 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,955 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,955 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,956 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:28,957 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:28,957 | ^~~~~~~ 2023-09-12T10:56:28,958 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,959 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,960 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,960 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:28,961 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,962 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,963 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,964 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:56:28,964 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,965 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:28,965 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,966 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,966 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:28,967 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:28,967 | ^~~~~~~ 2023-09-12T10:56:28,968 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:28,968 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,969 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:28,970 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,970 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,971 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,972 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:56:28,973 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,973 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:28,974 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,975 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,976 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:28,977 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:28,977 | ^~~~~~~ 2023-09-12T10:56:28,978 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:56:28,979 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:28,980 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,981 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,981 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,982 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:56:28,983 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,983 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:56:28,984 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,985 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,986 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:28,987 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:28,987 | ^~~~~~~ 2023-09-12T10:56:28,988 In copy constructor ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’, 2023-09-12T10:56:28,989 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:28,990 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:28,991 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:28,991 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:56:28,992 include/forcefields/forcefieldgaff.h:55:9: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:28,992 55 | class OBFFOOPCalculationGaff : public OBFFCalculation4 2023-09-12T10:56:28,993 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:28,994 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:28,994 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:28,995 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:28,996 | ^~~~~~~ 2023-09-12T10:56:28,997 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:28,997 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:28,998 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:28,999 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:29,000 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:29,000 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:29,001 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:29,002 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:56:29,003 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:29,003 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:29,004 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:29,005 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:29,006 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:29,007 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:29,007 | ^~~~~~~ 2023-09-12T10:56:29,008 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:29,009 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:29,010 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:29,011 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:29,011 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:29,012 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:29,013 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:29,014 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:56:29,015 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:29,015 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:29,016 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:29,017 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:29,017 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:29,018 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:29,018 | ^~~~~~~ 2023-09-12T10:56:29,019 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:29,019 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:29,020 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:29,021 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:29,021 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:29,022 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:29,023 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:29,023 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:56:29,024 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:29,025 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:29,025 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:29,026 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:29,026 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:29,027 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:29,028 | ^~~~~~~ 2023-09-12T10:56:29,028 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:29,029 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:29,029 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:29,030 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:29,031 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:29,031 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:29,032 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:56:29,032 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:29,033 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:29,033 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:29,034 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:29,034 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:29,035 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:29,035 | ^~~~~~~ 2023-09-12T10:56:29,036 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:56:29,037 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:56:29,037 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:29,038 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:29,039 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:29,039 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:56:29,040 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:29,040 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:56:29,041 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:29,042 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:29,042 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:29,043 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:29,044 | ^~~~~~~ 2023-09-12T10:56:29,044 In copy constructor ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’, 2023-09-12T10:56:29,045 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:29,045 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationGaff; _Args = {const OpenBabel::OBFFOOPCalculationGaff&}; _Tp = OpenBabel::OBFFOOPCalculationGaff]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:29,046 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:29,046 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:56:29,047 include/forcefields/forcefieldgaff.h:55:9: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:29,047 55 | class OBFFOOPCalculationGaff : public OBFFCalculation4 2023-09-12T10:56:29,048 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:29,048 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:56:29,049 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:56:29,049 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:56:29,050 | ^~~~~~~ 2023-09-12T10:56:29,051 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,051 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:56:29,052 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,053 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,053 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,054 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,054 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:56:29,055 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,056 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,056 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,057 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,057 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:56:29,058 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,059 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,060 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,060 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,061 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:56:29,061 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,061 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,062 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,062 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,063 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:56:29,063 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,064 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,064 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,065 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,066 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:56:29,066 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,067 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,068 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,068 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,069 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:56:29,070 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,070 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,071 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,071 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,072 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:806:28: 2023-09-12T10:56:29,072 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,073 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,074 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,074 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,075 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:820:28: 2023-09-12T10:56:29,075 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,076 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,076 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,077 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,077 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2023-09-12T10:56:29,078 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,078 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,078 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:29,079 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:56:29,080 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:1047:45: 2023-09-12T10:56:29,080 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:29,081 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:29,081 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:31,048 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:56:31,049 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:31,050 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:31,050 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,046 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,047 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,048 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1092:34: 2023-09-12T10:56:34,048 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,049 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,050 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,050 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,051 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,052 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1093:34: 2023-09-12T10:56:34,053 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,053 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,054 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,054 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,055 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,055 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1105:34: 2023-09-12T10:56:34,056 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,056 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,057 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,058 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,058 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,059 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1106:34: 2023-09-12T10:56:34,059 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,060 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,060 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,061 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,062 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,062 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1118:34: 2023-09-12T10:56:34,063 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,064 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,064 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,065 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,066 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,066 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1119:34: 2023-09-12T10:56:34,067 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,067 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,068 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,069 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,069 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,070 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1135:34: 2023-09-12T10:56:34,071 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,071 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,072 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,072 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,073 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,074 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1136:34: 2023-09-12T10:56:34,074 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,075 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,076 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,077 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,078 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,078 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1137:34: 2023-09-12T10:56:34,079 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,080 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,080 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,081 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,082 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,082 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1162:34: 2023-09-12T10:56:34,083 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,084 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,085 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,085 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,086 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,086 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1163:34: 2023-09-12T10:56:34,087 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,087 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,088 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,088 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,089 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,089 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1164:34: 2023-09-12T10:56:34,090 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,090 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,091 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,092 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,092 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,093 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1175:34: 2023-09-12T10:56:34,094 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,095 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,096 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,096 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,097 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,098 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1176:34: 2023-09-12T10:56:34,099 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,100 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,100 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,101 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,102 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,103 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1194:34: 2023-09-12T10:56:34,104 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,104 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,105 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:34,105 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:34,106 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:34,106 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1195:34: 2023-09-12T10:56:34,107 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:34,107 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:34,107 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:38,351 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldgaff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:56:38,352 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldgaff.o /tmp/ccvaB7k6.s 2023-09-12T10:56:38,360 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:39,495 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:56:39,495 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:56:39,496 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldgaff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldgaff.' 2023-09-12T10:56:39,500 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/forcefields/forcefieldghemical.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldghemical.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:56:39,505 Using built-in specs. 2023-09-12T10:56:39,506 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:39,506 Target: arm-linux-gnueabihf 2023-09-12T10:56:39,507 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:56:39,507 Thread model: posix 2023-09-12T10:56:39,508 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:39,508 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:39,509 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldghemical.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:56:39,509 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldghemical.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/forcefields/ -dumpbase forcefieldghemical.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccVtfS8P.s 2023-09-12T10:56:39,519 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:39,519 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:39,520 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:39,521 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:39,521 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:39,522 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:39,523 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:39,523 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:39,524 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:39,525 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:39,525 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:39,526 #include "..." search starts here: 2023-09-12T10:56:39,527 #include <...> search starts here: 2023-09-12T10:56:39,527 /usr/include/eigen3 2023-09-12T10:56:39,528 include 2023-09-12T10:56:39,528 /usr/include/python3.11 2023-09-12T10:56:39,529 /usr/include/c++/12 2023-09-12T10:56:39,529 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:39,529 /usr/include/c++/12/backward 2023-09-12T10:56:39,530 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:39,530 /usr/local/include 2023-09-12T10:56:39,531 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:39,531 /usr/include 2023-09-12T10:56:39,531 End of search list. 2023-09-12T10:56:39,532 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:39,532 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:39,533 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:39,534 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:39,538 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:41,109 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:41,110 from include/openbabel/mol.h:43, 2023-09-12T10:56:41,110 from ./src/forcefields/forcefieldghemical.cpp:20: 2023-09-12T10:56:41,111 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:41,111 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:41,112 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:41,113 | ^ 2023-09-12T10:56:41,113 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:41,114 37 | # define UNUSED(x) x 2023-09-12T10:56:41,115 | ^ 2023-09-12T10:56:41,876 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:41,876 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:41,877 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:41,878 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:41,878 | ^ 2023-09-12T10:56:41,879 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:41,880 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:41,881 | ^~~~~~~~ 2023-09-12T10:56:41,881 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:41,882 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:41,883 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:41,883 | ^ 2023-09-12T10:56:41,884 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:41,885 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:41,885 | ^~~~~~~~ 2023-09-12T10:56:41,900 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:41,901 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:41,902 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:41,902 | ^ 2023-09-12T10:56:41,903 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:41,904 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:41,904 | ^~~~~~~~ 2023-09-12T10:56:41,907 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:41,907 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:41,908 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:41,908 | ^ 2023-09-12T10:56:41,909 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:41,910 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:41,910 | ^~~~~~~~ 2023-09-12T10:56:42,220 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:56:42,221 from include/forcefields/forcefieldghemical.h:23, 2023-09-12T10:56:42,222 from ./src/forcefields/forcefieldghemical.cpp:23: 2023-09-12T10:56:42,223 include/openbabel/plugin.h: At global scope: 2023-09-12T10:56:42,224 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:42,224 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:42,225 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:42,226 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:56:42,227 from /usr/include/c++/12/vector:66, 2023-09-12T10:56:42,227 from include/openbabel/mol.h:35: 2023-09-12T10:56:42,228 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:42,229 131 | struct binary_function 2023-09-12T10:56:42,229 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:42,348 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:56:42,348 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,349 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,350 | ^ 2023-09-12T10:56:42,351 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,351 37 | # define UNUSED(x) x 2023-09-12T10:56:42,352 | ^ 2023-09-12T10:56:42,353 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:56:42,354 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,355 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,356 | ^ 2023-09-12T10:56:42,356 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,357 37 | # define UNUSED(x) x 2023-09-12T10:56:42,357 | ^ 2023-09-12T10:56:42,358 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:56:42,358 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,359 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,360 | ^ 2023-09-12T10:56:42,360 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,361 37 | # define UNUSED(x) x 2023-09-12T10:56:42,361 | ^ 2023-09-12T10:56:42,362 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:56:42,363 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,363 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,364 | ^ 2023-09-12T10:56:42,364 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,365 37 | # define UNUSED(x) x 2023-09-12T10:56:42,365 | ^ 2023-09-12T10:56:42,366 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:56:42,367 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,367 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,368 | ^ 2023-09-12T10:56:42,369 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,370 37 | # define UNUSED(x) x 2023-09-12T10:56:42,371 | ^ 2023-09-12T10:56:42,371 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:56:42,372 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,373 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,373 | ^ 2023-09-12T10:56:42,374 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,375 37 | # define UNUSED(x) x 2023-09-12T10:56:42,376 | ^ 2023-09-12T10:56:42,376 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:56:42,377 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,378 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,378 | ^ 2023-09-12T10:56:42,379 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,380 37 | # define UNUSED(x) x 2023-09-12T10:56:42,380 | ^ 2023-09-12T10:56:42,381 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:56:42,382 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:56:42,383 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:56:42,383 | ^ 2023-09-12T10:56:42,384 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,385 37 | # define UNUSED(x) x 2023-09-12T10:56:42,385 | ^ 2023-09-12T10:56:49,885 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:56:49,886 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’: 2023-09-12T10:56:49,886 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:49,887 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:49,888 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:50,030 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’: 2023-09-12T10:56:50,031 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:50,225 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’: 2023-09-12T10:56:50,226 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:50,438 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:56:50,439 /usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’: 2023-09-12T10:56:50,440 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:50,440 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:50,441 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:50,540 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’: 2023-09-12T10:56:50,540 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:50,541 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:50,542 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:50,687 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’: 2023-09-12T10:56:50,688 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:51,373 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,374 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:56:51,374 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,375 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,375 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,376 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:56:51,376 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,377 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,377 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,378 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,379 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,379 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,380 | ^~~~~~~~ 2023-09-12T10:56:51,381 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,382 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:56:51,382 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,383 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,384 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,385 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:56:51,385 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,386 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,387 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,388 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,389 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,389 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,390 | ^~~~~~~~ 2023-09-12T10:56:51,390 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,391 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:56:51,391 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,392 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,392 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,393 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:56:51,394 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,394 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,395 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,395 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,396 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,397 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,397 | ^~~~~~~~ 2023-09-12T10:56:51,398 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:56:51,398 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,399 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,399 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,400 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:56:51,401 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,401 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:56:51,402 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,402 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,403 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,403 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,404 | ^~~~~~~~ 2023-09-12T10:56:51,404 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:56:51,404 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,405 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,405 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,405 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:56:51,406 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,406 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:56:51,407 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,407 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,408 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,408 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,409 | ^~~~~~~~ 2023-09-12T10:56:51,409 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,410 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:56:51,411 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,411 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,412 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,413 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:56:51,414 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,415 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,415 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,416 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,416 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,417 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,418 | ^~~~~~~~ 2023-09-12T10:56:51,418 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,419 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:56:51,419 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,420 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,421 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,422 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:56:51,423 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,423 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,424 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,425 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,426 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,427 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,427 | ^~~~~~~~ 2023-09-12T10:56:51,428 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,429 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:56:51,430 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,431 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,431 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,433 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:56:51,433 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,434 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,435 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,435 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,436 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,436 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,437 | ^~~~~~~~ 2023-09-12T10:56:51,438 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:56:51,439 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,439 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,440 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,441 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:56:51,442 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,442 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:56:51,443 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,444 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,445 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,445 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,446 | ^~~~~~~~ 2023-09-12T10:56:51,447 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:56:51,447 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,448 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGhemical; _Args = {const OpenBabel::OBFFBondCalculationGhemical&}; _Tp = OpenBabel::OBFFBondCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,449 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,452 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:56:51,453 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,453 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:56:51,454 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,454 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,455 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:56:51,455 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:56:51,456 | ^~~~~~~~ 2023-09-12T10:56:51,456 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,457 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,458 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,458 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,459 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,460 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,460 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:56:51,461 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,462 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,463 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,463 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,464 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,465 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,465 | ^~~~~~~~~ 2023-09-12T10:56:51,466 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,467 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,468 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,469 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,469 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,470 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,470 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:56:51,471 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,472 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,473 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,474 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,474 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,475 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,476 | ^~~~~~~~~ 2023-09-12T10:56:51,477 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,478 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,479 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,480 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,481 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,481 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,482 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:56:51,483 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,484 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,485 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,486 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,486 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,487 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,487 | ^~~~~~~~~ 2023-09-12T10:56:51,488 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:51,488 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,489 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,490 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,490 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,491 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:56:51,491 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,492 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:51,493 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,494 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,494 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,495 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,496 | ^~~~~~~~~ 2023-09-12T10:56:51,496 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:56:51,497 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,498 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,498 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,499 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:56:51,500 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,500 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:56:51,501 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,502 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,502 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,503 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,503 | ^~~~~~~~~ 2023-09-12T10:56:51,504 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:56:51,504 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,505 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,505 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,506 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:56:51,507 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,508 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:56:51,508 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,509 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,510 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,511 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,512 | ^~~~~~~~~ 2023-09-12T10:56:51,512 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,513 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,514 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,515 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,515 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,516 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,517 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:56:51,518 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,518 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,519 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,519 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,520 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,520 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,521 | ^~~~~~~~~ 2023-09-12T10:56:51,521 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,522 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,522 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,523 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,524 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,524 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,525 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:56:51,526 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,526 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,527 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,528 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,528 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,529 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,529 | ^~~~~~~~~ 2023-09-12T10:56:51,530 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,531 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,532 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,532 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,533 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,533 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,534 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:56:51,534 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,535 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,535 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,536 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,537 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,538 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,538 | ^~~~~~~~~ 2023-09-12T10:56:51,539 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:51,540 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:56:51,541 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,542 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,542 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,543 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:56:51,544 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,545 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:51,546 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,546 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,547 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,547 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,548 | ^~~~~~~~~ 2023-09-12T10:56:51,548 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:56:51,549 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,549 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,550 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,550 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:56:51,551 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,552 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:56:51,552 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,553 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,554 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,555 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,555 | ^~~~~~~~~ 2023-09-12T10:56:51,556 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:56:51,557 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,558 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationGhemical; _Args = {const OpenBabel::OBFFAngleCalculationGhemical&}; _Tp = OpenBabel::OBFFAngleCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,559 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,559 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:56:51,560 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,561 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:56:51,562 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,562 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,563 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:56:51,564 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:56:51,564 | ^~~~~~~~~ 2023-09-12T10:56:51,565 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,566 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,566 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:51,567 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:56:51,568 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,568 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,569 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,570 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:56:51,570 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,571 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,572 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,572 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,573 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:56:51,574 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:56:51,574 | ^~~~~~~~~~~ 2023-09-12T10:56:51,575 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,576 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,577 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:51,577 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:56:51,578 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,579 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,580 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,580 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:56:51,581 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,582 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,582 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,583 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,584 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:56:51,585 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:56:51,585 | ^~~~~~~~~~~ 2023-09-12T10:56:51,586 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,587 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:56:51,588 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:51,589 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:56:51,590 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,591 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,591 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,592 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:56:51,593 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,594 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,595 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,595 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,596 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:56:51,597 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:56:51,597 | ^~~~~~~~~~~ 2023-09-12T10:56:51,598 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:56:51,598 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:56:51,599 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:56:51,600 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,600 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,601 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,601 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:56:51,602 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,603 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:56:51,604 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,604 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,605 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:56:51,606 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:56:51,606 | ^~~~~~~~~~~ 2023-09-12T10:56:51,607 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:56:51,607 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:56:51,608 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,608 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,610 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,610 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:56:51,610 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,611 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:56:51,611 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,612 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,612 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:56:51,613 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:56:51,613 | ^~~~~~~~~~~ 2023-09-12T10:56:51,614 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’, 2023-09-12T10:56:51,614 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,615 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationGhemical; _Args = {const OpenBabel::OBFFTorsionCalculationGhemical&}; _Tp = OpenBabel::OBFFTorsionCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,615 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,616 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:56:51,617 include/forcefields/forcefieldghemical.h:46:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,617 46 | class OBFFTorsionCalculationGhemical : public OBFFCalculation4 2023-09-12T10:56:51,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,618 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,619 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:56:51,620 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:56:51,620 | ^~~~~~~~~~~ 2023-09-12T10:56:51,621 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,621 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2023-09-12T10:56:51,622 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,623 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,623 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,624 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:56:51,624 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,625 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,625 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,626 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,626 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:56:51,627 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:56:51,627 | ^~~~~~~ 2023-09-12T10:56:51,628 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,629 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2023-09-12T10:56:51,629 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,630 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,631 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,631 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:56:51,632 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,633 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,633 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,634 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,635 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:56:51,635 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:56:51,636 | ^~~~~~~ 2023-09-12T10:56:51,637 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,638 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2023-09-12T10:56:51,638 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,638 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,639 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,639 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:56:51,640 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,640 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,641 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,641 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,642 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:56:51,643 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:56:51,643 | ^~~~~~~ 2023-09-12T10:56:51,644 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2023-09-12T10:56:51,645 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,645 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,646 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,647 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:56:51,647 include/forcefields/forcefieldghemical.h:56:9: warning: ‘vdwcalc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,648 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2023-09-12T10:56:51,648 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,649 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,650 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:56:51,650 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:56:51,651 | ^~~~~~~ 2023-09-12T10:56:51,651 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2023-09-12T10:56:51,652 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,652 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGhemical; _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,653 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,653 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:56:51,654 include/forcefields/forcefieldghemical.h:56:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,654 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2023-09-12T10:56:51,655 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,655 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,656 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:56:51,656 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:56:51,657 | ^~~~~~~ 2023-09-12T10:56:51,658 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,658 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2023-09-12T10:56:51,659 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGhemical; _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,660 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGhemical; _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,660 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,661 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:56:51,662 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,662 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,663 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,664 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,664 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2023-09-12T10:56:51,665 780 | OBFFElectrostaticCalculationGhemical elecalc; 2023-09-12T10:56:51,665 | ^~~~~~~ 2023-09-12T10:56:51,666 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,666 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2023-09-12T10:56:51,667 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGhemical; _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,668 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGhemical; _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,668 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,669 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:56:51,670 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,671 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,671 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,672 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,673 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2023-09-12T10:56:51,674 780 | OBFFElectrostaticCalculationGhemical elecalc; 2023-09-12T10:56:51,675 | ^~~~~~~ 2023-09-12T10:56:51,675 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:56:51,676 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2023-09-12T10:56:51,677 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGhemical; _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:56:51,678 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGhemical; _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:56:51,679 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:56:51,680 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:56:51,680 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:51,681 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:56:51,681 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:56:51,682 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:56:51,682 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2023-09-12T10:56:51,683 780 | OBFFElectrostaticCalculationGhemical elecalc; 2023-09-12T10:56:51,683 | ^~~~~~~ 2023-09-12T10:56:51,684 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:56:51,684 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:56:51,685 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:51,685 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:51,686 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:51,687 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:56:51,688 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:56:51,689 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:51,689 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:51,690 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:51,691 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:56:51,692 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:56:51,692 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:51,693 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:51,694 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:51,695 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:56:51,696 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:56:51,696 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:51,698 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:51,698 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:51,699 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:56:51,699 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:56:51,700 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:51,701 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:51,701 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:51,702 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:56:51,703 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:56:51,704 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:51,704 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:51,705 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:51,706 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:56:51,707 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:56:51,708 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:51,709 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:56:51,710 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:56:53,175 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:56:53,175 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:53,176 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:53,177 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:55,639 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:55,639 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:55,640 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:870:34: 2023-09-12T10:56:55,641 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:55,641 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:55,642 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:55,643 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:55,644 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:55,644 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:871:34: 2023-09-12T10:56:55,645 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:55,645 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:55,646 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:55,646 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:55,647 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:55,648 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:888:34: 2023-09-12T10:56:55,648 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:55,649 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:55,650 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:55,650 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:55,651 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:55,652 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:889:34: 2023-09-12T10:56:55,653 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:55,654 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:55,655 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:55,655 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:55,656 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:55,657 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:920:34: 2023-09-12T10:56:55,657 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:55,658 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:55,659 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:55,660 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:55,661 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:55,661 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:921:34: 2023-09-12T10:56:55,662 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:55,662 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:55,663 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:55,663 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:55,664 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:56:55,665 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:933:34: 2023-09-12T10:56:55,665 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:56:55,666 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:55,667 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:58,382 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldghemical.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:56:58,382 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldghemical.o /tmp/ccVtfS8P.s 2023-09-12T10:56:58,387 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:59,395 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:56:59,396 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:56:59,396 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldghemical.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldghemical.' 2023-09-12T10:56:59,400 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/forcefields/forcefieldmm2.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmm2.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:56:59,405 Using built-in specs. 2023-09-12T10:56:59,406 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:59,406 Target: arm-linux-gnueabihf 2023-09-12T10:56:59,406 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:56:59,407 Thread model: posix 2023-09-12T10:56:59,407 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:59,408 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:59,409 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmm2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:56:59,409 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldmm2.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/forcefields/ -dumpbase forcefieldmm2.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccjeMGjl.s 2023-09-12T10:56:59,418 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:59,419 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:59,420 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:59,421 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:59,421 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:59,422 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:59,423 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:59,423 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:59,424 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:59,425 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:59,425 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:59,426 #include "..." search starts here: 2023-09-12T10:56:59,427 #include <...> search starts here: 2023-09-12T10:56:59,427 /usr/include/eigen3 2023-09-12T10:56:59,428 include 2023-09-12T10:56:59,428 /usr/include/python3.11 2023-09-12T10:56:59,428 /usr/include/c++/12 2023-09-12T10:56:59,429 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:59,429 /usr/include/c++/12/backward 2023-09-12T10:56:59,430 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:59,430 /usr/local/include 2023-09-12T10:56:59,431 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:59,431 /usr/include 2023-09-12T10:56:59,432 End of search list. 2023-09-12T10:56:59,432 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:59,433 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:59,434 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:59,434 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:59,439 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:59,787 In file included from ./src/forcefields/forcefieldmm2.cpp:21: 2023-09-12T10:56:59,788 include/forcefields/forcefieldmm2.h:68:57: warning: multi-line comment [-Wcomment] 2023-09-12T10:56:59,788 68 | // b = atom d \ 2023-09-12T10:56:59,789 | ^ 2023-09-12T10:56:59,790 ./src/forcefields/forcefieldmm2.cpp:276:3: warning: multi-line comment [-Wcomment] 2023-09-12T10:56:59,791 276 | // \ 2023-09-12T10:56:59,791 | ^ 2023-09-12T10:57:01,055 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:01,056 from include/openbabel/mol.h:43, 2023-09-12T10:57:01,057 from ./src/forcefields/forcefieldmm2.cpp:19: 2023-09-12T10:57:01,057 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:01,058 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:01,059 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:01,060 | ^ 2023-09-12T10:57:01,060 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:01,061 37 | # define UNUSED(x) x 2023-09-12T10:57:01,062 | ^ 2023-09-12T10:57:01,838 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:01,839 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:01,840 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:01,840 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:01,841 | ^ 2023-09-12T10:57:01,842 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:01,843 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:01,844 | ^~~~~~~~ 2023-09-12T10:57:01,844 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:01,845 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:01,846 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:01,847 | ^ 2023-09-12T10:57:01,848 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:01,848 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:01,849 | ^~~~~~~~ 2023-09-12T10:57:01,864 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:01,865 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:01,865 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:01,866 | ^ 2023-09-12T10:57:01,866 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:01,867 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:01,868 | ^~~~~~~~ 2023-09-12T10:57:01,871 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:01,871 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:01,872 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:01,873 | ^ 2023-09-12T10:57:01,874 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:01,875 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:01,876 | ^~~~~~~~ 2023-09-12T10:57:02,186 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:57:02,187 from include/forcefields/forcefieldmm2.h:23: 2023-09-12T10:57:02,188 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:02,188 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:02,189 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:02,189 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:02,190 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:02,191 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:02,191 from include/openbabel/mol.h:35: 2023-09-12T10:57:02,192 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:02,193 131 | struct binary_function 2023-09-12T10:57:02,194 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:02,315 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:57:02,315 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,316 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,317 | ^ 2023-09-12T10:57:02,318 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,318 37 | # define UNUSED(x) x 2023-09-12T10:57:02,319 | ^ 2023-09-12T10:57:02,320 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:57:02,320 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,321 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,321 | ^ 2023-09-12T10:57:02,322 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,322 37 | # define UNUSED(x) x 2023-09-12T10:57:02,323 | ^ 2023-09-12T10:57:02,323 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:57:02,324 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,325 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,325 | ^ 2023-09-12T10:57:02,326 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,326 37 | # define UNUSED(x) x 2023-09-12T10:57:02,327 | ^ 2023-09-12T10:57:02,327 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:57:02,328 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,329 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,329 | ^ 2023-09-12T10:57:02,330 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,330 37 | # define UNUSED(x) x 2023-09-12T10:57:02,331 | ^ 2023-09-12T10:57:02,332 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:57:02,333 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,333 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,334 | ^ 2023-09-12T10:57:02,335 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,336 37 | # define UNUSED(x) x 2023-09-12T10:57:02,336 | ^ 2023-09-12T10:57:02,337 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:57:02,338 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,338 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,339 | ^ 2023-09-12T10:57:02,339 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,340 37 | # define UNUSED(x) x 2023-09-12T10:57:02,341 | ^ 2023-09-12T10:57:02,341 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:57:02,342 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,343 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,343 | ^ 2023-09-12T10:57:02,344 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,345 37 | # define UNUSED(x) x 2023-09-12T10:57:02,346 | ^ 2023-09-12T10:57:02,346 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:57:02,347 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:02,347 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:02,348 | ^ 2023-09-12T10:57:02,349 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:02,349 37 | # define UNUSED(x) x 2023-09-12T10:57:02,350 | ^ 2023-09-12T10:57:02,365 include/forcefields/forcefieldmm2.h: In member function ‘virtual OpenBabel::OBForceFieldMM2* OpenBabel::OBForceFieldMM2::MakeNewInstance()’: 2023-09-12T10:57:02,366 include/forcefields/forcefieldmm2.h:97:83: warning: implicitly-declared ‘OpenBabel::OBForceFieldMM2::OBForceFieldMM2(const OpenBabel::OBForceFieldMM2&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:02,366 97 | virtual OBForceFieldMM2* MakeNewInstance(){ return new OBForceFieldMM2(*this); } 2023-09-12T10:57:02,367 | ^ 2023-09-12T10:57:02,367 include/forcefields/forcefieldmm2.h:107:24: note: because ‘OpenBabel::OBForceFieldMM2’ has user-provided ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’ 2023-09-12T10:57:02,368 107 | OBForceFieldMM2 &operator = (OBForceFieldMM2 &); 2023-09-12T10:57:02,368 | ^~~~~~~~ 2023-09-12T10:57:02,381 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_Angle()’: 2023-09-12T10:57:02,381 ./src/forcefields/forcefieldmm2.cpp:81:59: warning: variable ‘delta3’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:57:02,382 81 | double e, energy, force, ang, ang_ref, delta, delta2, delta3, delta4, f, dotprod, rab, rab2, rab3, rbc, rbc2, rbc3, root, dotprod_abbc; 2023-09-12T10:57:02,383 | ^~~~~~ 2023-09-12T10:57:02,396 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_OOP()’: 2023-09-12T10:57:02,397 ./src/forcefields/forcefieldmm2.cpp:292:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:02,398 292 | for (int idx=0; idx < _ffoutplanebendparams.size(); idx++) { 2023-09-12T10:57:02,399 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:03,816 ./src/forcefields/forcefieldmm2.cpp: In member function ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’: 2023-09-12T10:57:03,817 ./src/forcefields/forcefieldmm2.cpp:503:3: warning: control reaches end of non-void function [-Wreturn-type] 2023-09-12T10:57:03,818 503 | } 2023-09-12T10:57:03,819 | ^ 2023-09-12T10:57:07,415 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:57:07,416 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:57:07,416 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:07,417 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:07,418 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,954 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,955 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,956 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:600:34: 2023-09-12T10:57:07,956 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,957 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,958 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,958 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,959 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,959 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:601:34: 2023-09-12T10:57:07,960 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,961 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,961 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,962 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,963 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,964 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:614:34: 2023-09-12T10:57:07,964 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,965 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,966 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,967 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,967 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,968 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:615:34: 2023-09-12T10:57:07,969 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,969 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,970 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,971 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,972 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,972 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:621:34: 2023-09-12T10:57:07,973 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,974 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,975 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,976 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,976 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,977 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:632:34: 2023-09-12T10:57:07,978 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,978 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,979 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,979 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,980 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,981 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:633:34: 2023-09-12T10:57:07,981 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,982 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,983 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,984 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,985 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,985 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:634:34: 2023-09-12T10:57:07,986 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,987 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,987 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,988 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,989 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,989 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:641:34: 2023-09-12T10:57:07,990 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,991 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,992 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,992 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,993 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,994 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:648:34: 2023-09-12T10:57:07,994 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,995 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,995 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:07,996 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:07,997 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:07,997 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:649:34: 2023-09-12T10:57:07,998 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:07,999 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:07,999 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:08,000 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:08,001 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:08,002 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:655:34: 2023-09-12T10:57:08,003 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:08,003 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:08,004 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:08,005 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:08,005 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:08,006 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:656:34: 2023-09-12T10:57:08,006 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:08,007 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:08,008 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:08,008 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:08,009 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:08,010 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:663:34: 2023-09-12T10:57:08,010 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:08,011 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:08,011 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:08,012 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:08,012 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:08,013 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:664:34: 2023-09-12T10:57:08,013 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:08,014 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:08,014 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:10,444 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmm2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:57:10,444 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmm2.o /tmp/ccjeMGjl.s 2023-09-12T10:57:10,449 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:11,170 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:57:11,171 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:57:11,171 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmm2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmm2.' 2023-09-12T10:57:11,174 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/forcefields/forcefieldmmff94.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmmff94.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:57:11,179 Using built-in specs. 2023-09-12T10:57:11,180 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:11,180 Target: arm-linux-gnueabihf 2023-09-12T10:57:11,181 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:57:11,181 Thread model: posix 2023-09-12T10:57:11,181 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:11,182 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:11,182 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:57:11,183 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldmmff94.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/forcefields/ -dumpbase forcefieldmmff94.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cctZl1MR.s 2023-09-12T10:57:11,192 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:11,193 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:11,194 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:11,194 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:11,195 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:11,196 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:11,196 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:11,197 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:11,198 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:11,198 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:11,199 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:11,199 #include "..." search starts here: 2023-09-12T10:57:11,200 #include <...> search starts here: 2023-09-12T10:57:11,201 /usr/include/eigen3 2023-09-12T10:57:11,201 include 2023-09-12T10:57:11,202 /usr/include/python3.11 2023-09-12T10:57:11,202 /usr/include/c++/12 2023-09-12T10:57:11,203 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:11,203 /usr/include/c++/12/backward 2023-09-12T10:57:11,204 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:11,204 /usr/local/include 2023-09-12T10:57:11,205 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:11,205 /usr/include 2023-09-12T10:57:11,205 End of search list. 2023-09-12T10:57:11,206 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:11,206 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:11,207 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:11,208 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:11,212 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:12,798 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:12,798 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:12,799 from ./src/forcefields/forcefieldmmff94.cpp:31: 2023-09-12T10:57:12,799 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:12,800 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:12,800 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:12,801 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:57:12,802 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:57:12,803 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:57:12,803 from /usr/include/c++/12/ios:42, 2023-09-12T10:57:12,804 from /usr/include/c++/12/ostream:38, 2023-09-12T10:57:12,805 from /usr/include/c++/12/iostream:39, 2023-09-12T10:57:12,806 from include/openbabel/obconversion.h:24: 2023-09-12T10:57:12,806 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:12,807 131 | struct binary_function 2023-09-12T10:57:12,808 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:13,026 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:13,027 from include/openbabel/mol.h:43, 2023-09-12T10:57:13,028 from ./src/forcefields/forcefieldmmff94.cpp:32: 2023-09-12T10:57:13,029 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:13,029 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:13,030 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:13,031 | ^ 2023-09-12T10:57:13,031 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:13,032 37 | # define UNUSED(x) x 2023-09-12T10:57:13,033 | ^ 2023-09-12T10:57:13,708 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:13,709 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,710 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,710 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:13,711 | ^ 2023-09-12T10:57:13,712 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:13,713 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:13,713 | ^~~~~~~~ 2023-09-12T10:57:13,714 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,715 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,715 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:13,716 | ^ 2023-09-12T10:57:13,716 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:13,717 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:13,717 | ^~~~~~~~ 2023-09-12T10:57:13,735 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,736 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,736 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:13,737 | ^ 2023-09-12T10:57:13,738 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:13,738 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:13,739 | ^~~~~~~~ 2023-09-12T10:57:13,742 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,742 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,743 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:13,744 | ^ 2023-09-12T10:57:13,745 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:13,745 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:13,746 | ^~~~~~~~ 2023-09-12T10:57:14,165 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:57:14,166 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,167 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,167 | ^ 2023-09-12T10:57:14,168 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,169 37 | # define UNUSED(x) x 2023-09-12T10:57:14,169 | ^ 2023-09-12T10:57:14,170 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:57:14,171 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,172 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,173 | ^ 2023-09-12T10:57:14,173 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,174 37 | # define UNUSED(x) x 2023-09-12T10:57:14,174 | ^ 2023-09-12T10:57:14,175 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:57:14,175 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,176 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,177 | ^ 2023-09-12T10:57:14,177 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,178 37 | # define UNUSED(x) x 2023-09-12T10:57:14,178 | ^ 2023-09-12T10:57:14,179 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:57:14,179 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,180 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,181 | ^ 2023-09-12T10:57:14,181 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,182 37 | # define UNUSED(x) x 2023-09-12T10:57:14,183 | ^ 2023-09-12T10:57:14,183 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:57:14,184 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,185 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,186 | ^ 2023-09-12T10:57:14,187 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,187 37 | # define UNUSED(x) x 2023-09-12T10:57:14,188 | ^ 2023-09-12T10:57:14,189 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:57:14,190 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,190 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,191 | ^ 2023-09-12T10:57:14,192 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,192 37 | # define UNUSED(x) x 2023-09-12T10:57:14,193 | ^ 2023-09-12T10:57:14,194 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:57:14,194 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,195 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,196 | ^ 2023-09-12T10:57:14,196 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,197 37 | # define UNUSED(x) x 2023-09-12T10:57:14,198 | ^ 2023-09-12T10:57:14,198 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:57:14,199 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:14,200 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:14,201 | ^ 2023-09-12T10:57:14,201 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:14,202 37 | # define UNUSED(x) x 2023-09-12T10:57:14,202 | ^ 2023-09-12T10:57:14,502 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:14,502 ./src/forcefields/forcefieldmmff94.cpp:2790:32: warning: variable ‘bondtype1’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:57:14,503 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2023-09-12T10:57:14,503 | ^~~~~~~~~ 2023-09-12T10:57:14,504 ./src/forcefields/forcefieldmmff94.cpp:2790:43: warning: variable ‘bondtype2’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:57:14,504 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2023-09-12T10:57:14,505 | ^~~~~~~~~ 2023-09-12T10:57:14,980 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = true]’: 2023-09-12T10:57:14,981 include/forcefields/forcefieldmmff94.h:288:40: required from here 2023-09-12T10:57:14,981 ./src/forcefields/forcefieldmmff94.cpp:140:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:14,982 140 | for (int i = 0; i < _bondcalculations.size(); ++i) { 2023-09-12T10:57:14,983 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:14,984 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = false]’: 2023-09-12T10:57:14,984 include/forcefields/forcefieldmmff94.h:288:58: required from here 2023-09-12T10:57:14,985 ./src/forcefields/forcefieldmmff94.cpp:140:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:14,987 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = true]’: 2023-09-12T10:57:14,987 include/forcefields/forcefieldmmff94.h:294:41: required from here 2023-09-12T10:57:14,988 ./src/forcefields/forcefieldmmff94.cpp:255:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:14,989 255 | for (int i = 0; i < _anglecalculations.size(); ++i) { 2023-09-12T10:57:14,990 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:14,990 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = false]’: 2023-09-12T10:57:14,991 include/forcefields/forcefieldmmff94.h:294:60: required from here 2023-09-12T10:57:14,991 ./src/forcefields/forcefieldmmff94.cpp:255:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:14,993 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = true]’: 2023-09-12T10:57:14,994 include/forcefields/forcefieldmmff94.h:300:42: required from here 2023-09-12T10:57:14,995 ./src/forcefields/forcefieldmmff94.cpp:368:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:14,995 368 | for (int i = 0; i < _strbndcalculations.size(); ++i) { 2023-09-12T10:57:14,996 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:14,997 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = false]’: 2023-09-12T10:57:14,998 include/forcefields/forcefieldmmff94.h:300:62: required from here 2023-09-12T10:57:14,998 ./src/forcefields/forcefieldmmff94.cpp:368:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,000 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = true]’: 2023-09-12T10:57:15,000 include/forcefields/forcefieldmmff94.h:306:43: required from here 2023-09-12T10:57:15,001 ./src/forcefields/forcefieldmmff94.cpp:504:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,002 504 | for (int i = 0; i < _torsioncalculations.size(); ++i) { 2023-09-12T10:57:15,002 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:15,004 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = false]’: 2023-09-12T10:57:15,004 include/forcefields/forcefieldmmff94.h:306:64: required from here 2023-09-12T10:57:15,005 ./src/forcefields/forcefieldmmff94.cpp:504:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,007 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = true]’: 2023-09-12T10:57:15,008 include/forcefields/forcefieldmmff94.h:312:39: required from here 2023-09-12T10:57:15,009 ./src/forcefields/forcefieldmmff94.cpp:602:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,009 602 | for (int i = 0; i < _oopcalculations.size(); ++i) { 2023-09-12T10:57:15,010 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:15,011 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = false]’: 2023-09-12T10:57:15,012 include/forcefields/forcefieldmmff94.h:312:56: required from here 2023-09-12T10:57:15,012 ./src/forcefields/forcefieldmmff94.cpp:602:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,014 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = true]’: 2023-09-12T10:57:15,015 include/forcefields/forcefieldmmff94.h:318:39: required from here 2023-09-12T10:57:15,016 ./src/forcefields/forcefieldmmff94.cpp:699:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,016 699 | for (int i = 0; i < _vdwcalculations.size(); ++i) { 2023-09-12T10:57:15,017 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:15,018 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = false]’: 2023-09-12T10:57:15,019 include/forcefields/forcefieldmmff94.h:318:56: required from here 2023-09-12T10:57:15,020 ./src/forcefields/forcefieldmmff94.cpp:699:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,020 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = true]’: 2023-09-12T10:57:15,021 include/forcefields/forcefieldmmff94.h:324:49: required from here 2023-09-12T10:57:15,022 ./src/forcefields/forcefieldmmff94.cpp:785:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:15,022 785 | for (int i = 0; i < _electrostaticcalculations.size(); ++i) { 2023-09-12T10:57:15,023 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:15,024 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = false]’: 2023-09-12T10:57:15,024 include/forcefields/forcefieldmmff94.h:324:76: required from here 2023-09-12T10:57:15,025 ./src/forcefields/forcefieldmmff94.cpp:785:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:57:16,549 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘int OpenBabel::OBForceFieldMMFF94::GetStrBndType(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*)’: 2023-09-12T10:57:16,550 ./src/forcefields/forcefieldmmff94.cpp:4540:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:57:16,550 4540 | if (btbc) { 2023-09-12T10:57:16,551 | ^~ 2023-09-12T10:57:16,552 ./src/forcefields/forcefieldmmff94.cpp:4548:5: note: here 2023-09-12T10:57:16,553 4548 | case 2: 2023-09-12T10:57:16,553 | ^~~~ 2023-09-12T10:57:16,554 ./src/forcefields/forcefieldmmff94.cpp:4565:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:57:16,555 4565 | if (btbc) { 2023-09-12T10:57:16,555 | ^~ 2023-09-12T10:57:16,556 ./src/forcefields/forcefieldmmff94.cpp:4573:5: note: here 2023-09-12T10:57:16,557 4573 | case 6: 2023-09-12T10:57:16,557 | ^~~~ 2023-09-12T10:57:16,558 ./src/forcefields/forcefieldmmff94.cpp:4584:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:57:16,559 4584 | if (btbc) { 2023-09-12T10:57:16,560 | ^~ 2023-09-12T10:57:16,560 ./src/forcefields/forcefieldmmff94.cpp:4592:5: note: here 2023-09-12T10:57:16,561 4592 | case 8: 2023-09-12T10:57:16,561 | ^~~~ 2023-09-12T10:57:20,861 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘bool OpenBabel::OBForceFieldMMFF94::PerceiveAromatic()’: 2023-09-12T10:57:20,862 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘first_rj’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:20,862 1443 | ringbond = _mol.GetBond(first_rj, index); 2023-09-12T10:57:20,863 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:57:20,864 ./src/forcefields/forcefieldmmff94.cpp:1380:29: note: ‘first_rj’ was declared here 2023-09-12T10:57:20,865 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2023-09-12T10:57:20,865 | ^~~~~~~~ 2023-09-12T10:57:20,866 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:20,867 1443 | ringbond = _mol.GetBond(first_rj, index); 2023-09-12T10:57:20,868 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:57:20,869 ./src/forcefields/forcefieldmmff94.cpp:1380:12: note: ‘index’ was declared here 2023-09-12T10:57:20,869 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2023-09-12T10:57:20,870 | ^~~~~ 2023-09-12T10:57:24,029 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:57:24,031 from include/openbabel/obconversion.h:30: 2023-09-12T10:57:24,032 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:24,034 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:24,035 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:24,036 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:24,179 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:24,180 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:24,390 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:24,390 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:25,168 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:25,169 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:25,412 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFOOPCalculationMMFF94&}; _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:25,412 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:25,587 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:57:25,587 /usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:25,588 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:25,589 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:25,590 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:25,689 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFVDWCalculationMMFF94&}; _Tp = OpenBabel::OBFFVDWCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:25,690 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:25,691 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:25,691 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:25,870 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFElectrostaticCalculationMMFF94&}; _Tp = OpenBabel::OBFFElectrostaticCalculationMMFF94; _Alloc = std::allocator]’: 2023-09-12T10:57:25,871 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:26,818 In file included from include/forcefields/forcefieldmmff94.h:24, 2023-09-12T10:57:26,819 from ./src/forcefields/forcefieldmmff94.cpp:36: 2023-09-12T10:57:26,819 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,820 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:57:26,820 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,821 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,822 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,822 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:57:26,823 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,824 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,824 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,825 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,826 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,826 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,827 | ^~~~~~~~ 2023-09-12T10:57:26,828 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,828 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:57:26,829 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,830 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,831 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,832 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:57:26,832 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,833 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,833 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,834 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,834 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,835 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,836 | ^~~~~~~~ 2023-09-12T10:57:26,836 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,837 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:57:26,838 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,839 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,839 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,840 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:57:26,840 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,841 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,841 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,842 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,842 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,843 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,843 | ^~~~~~~~ 2023-09-12T10:57:26,844 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:57:26,845 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,845 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,845 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,846 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:57:26,846 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,847 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:57:26,847 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,847 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,848 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,848 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,848 | ^~~~~~~~ 2023-09-12T10:57:26,849 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:57:26,849 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,850 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,851 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,851 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:57:26,852 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,852 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:57:26,853 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,853 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,854 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,854 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,855 | ^~~~~~~~ 2023-09-12T10:57:26,855 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,856 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:57:26,856 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,857 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,857 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,858 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:57:26,858 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,859 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,859 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,860 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,860 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,861 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,861 | ^~~~~~~~ 2023-09-12T10:57:26,862 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,862 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:57:26,863 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,863 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,864 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,864 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:57:26,865 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,865 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,866 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,866 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,867 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,868 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,868 | ^~~~~~~~ 2023-09-12T10:57:26,869 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,869 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:57:26,869 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,870 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,870 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,870 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:57:26,871 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,871 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,872 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,872 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,873 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,873 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,874 | ^~~~~~~~ 2023-09-12T10:57:26,874 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:57:26,875 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,875 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,876 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,876 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:57:26,877 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,877 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:57:26,878 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,878 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,879 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,880 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,880 | ^~~~~~~~ 2023-09-12T10:57:26,880 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:57:26,881 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,881 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationMMFF94; _Args = {const OpenBabel::OBFFBondCalculationMMFF94&}; _Tp = OpenBabel::OBFFBondCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,881 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,882 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:57:26,882 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,882 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:57:26,883 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,884 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,884 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:57:26,885 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:57:26,886 | ^~~~~~~~ 2023-09-12T10:57:26,886 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,887 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:26,888 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:57:26,888 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,889 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,890 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,890 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:57:26,891 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,891 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,892 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,892 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,893 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:57:26,893 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:57:26,893 | ^~~~~~~~~ 2023-09-12T10:57:26,894 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,894 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:26,894 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:57:26,895 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,895 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,895 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,896 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:57:26,897 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,897 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,898 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,898 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,898 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:57:26,899 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:57:26,899 | ^~~~~~~~~ 2023-09-12T10:57:26,900 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,900 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:26,901 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:57:26,901 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,902 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,903 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,903 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:57:26,903 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,904 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,904 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,904 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,905 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:57:26,905 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:57:26,905 | ^~~~~~~~~ 2023-09-12T10:57:26,906 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:57:26,906 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:57:26,906 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,907 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,908 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,908 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:57:26,909 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,909 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:57:26,910 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,910 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,911 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:57:26,912 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:57:26,912 | ^~~~~~~~~ 2023-09-12T10:57:26,913 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2023-09-12T10:57:26,914 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,915 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,915 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,916 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:57:26,916 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,917 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:26,917 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,918 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,918 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:57:26,919 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:57:26,919 | ^~~~~~~~~ 2023-09-12T10:57:26,920 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2023-09-12T10:57:26,921 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,922 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,923 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,923 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:57:26,924 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,925 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:26,926 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,926 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,927 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:57:26,928 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:57:26,929 | ^~~~~~~~~ 2023-09-12T10:57:26,929 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,930 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:26,931 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:57:26,932 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,933 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,933 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,934 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,934 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,935 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,935 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,936 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,937 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,937 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,938 | ^~~~~~~~~~ 2023-09-12T10:57:26,939 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,939 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:26,940 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:57:26,941 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,942 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,942 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,943 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,944 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,945 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,946 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,946 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,947 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,947 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,948 | ^~~~~~~~~~ 2023-09-12T10:57:26,949 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:26,949 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:26,950 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:57:26,951 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,951 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,952 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,953 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,954 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,955 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:26,956 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,956 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,957 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,958 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,959 | ^~~~~~~~~~ 2023-09-12T10:57:26,959 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:57:26,960 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:57:26,961 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,962 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,963 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,964 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,964 include/openbabel/forcefield.h:170:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,965 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:57:26,966 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,966 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,967 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,967 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,968 | ^~~~~~~~~~ 2023-09-12T10:57:26,968 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:26,969 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,969 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,970 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,971 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,971 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,972 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:26,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,974 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,974 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,975 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,975 | ^~~~~~~~~~ 2023-09-12T10:57:26,976 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:26,977 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,977 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,978 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,979 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,980 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,980 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:26,981 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,981 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,982 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,982 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,983 | ^~~~~~~~~~ 2023-09-12T10:57:26,983 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:26,984 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,985 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,985 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,986 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,987 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,987 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:26,988 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,989 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,989 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,990 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,991 | ^~~~~~~~~~ 2023-09-12T10:57:26,991 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:26,992 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:26,993 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:26,994 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:26,995 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:26,995 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:26,996 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:26,996 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:26,997 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:26,998 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:26,998 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:26,999 | ^~~~~~~~~~ 2023-09-12T10:57:26,999 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,000 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,000 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,001 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,002 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,003 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,003 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,004 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,005 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,006 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,007 | ^~~~~~~~~~ 2023-09-12T10:57:27,007 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,008 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,009 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,010 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,011 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,011 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,012 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,013 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,014 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,014 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,015 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,016 | ^~~~~~~~~~ 2023-09-12T10:57:27,016 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,017 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,017 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,018 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,019 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,019 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,020 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,021 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,022 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,023 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,024 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,024 | ^~~~~~~~~~ 2023-09-12T10:57:27,025 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,026 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,027 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,028 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,029 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,029 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,030 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,031 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,032 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,032 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,033 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,033 | ^~~~~~~~~~ 2023-09-12T10:57:27,034 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,034 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,035 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,036 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,036 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,037 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,038 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,038 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,039 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,039 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,040 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,041 | ^~~~~~~~~~ 2023-09-12T10:57:27,041 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,042 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,043 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,043 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,044 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,044 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,045 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,046 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,046 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,047 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,047 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,048 | ^~~~~~~~~~ 2023-09-12T10:57:27,049 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,049 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,050 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,051 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,052 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,053 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,053 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,054 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,054 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,055 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,056 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,056 | ^~~~~~~~~~ 2023-09-12T10:57:27,057 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,058 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,059 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,060 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,061 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,062 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,062 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,063 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,063 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,064 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,065 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,065 | ^~~~~~~~~~ 2023-09-12T10:57:27,066 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:57:27,067 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,068 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,069 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,070 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,070 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,071 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:57:27,072 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,072 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,073 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:57:27,073 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:57:27,074 | ^~~~~~~~~~ 2023-09-12T10:57:27,075 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:27,075 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:27,076 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:57:27,077 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:57:27,077 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,078 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,078 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,079 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,079 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,080 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:27,080 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,081 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,081 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:57:27,082 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:57:27,083 | ^~~~~~~~~~~ 2023-09-12T10:57:27,083 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:27,084 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:27,085 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:57:27,086 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:57:27,086 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,087 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,087 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,088 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,089 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,089 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:27,090 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,090 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,091 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:57:27,091 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:57:27,091 | ^~~~~~~~~~~ 2023-09-12T10:57:27,092 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:27,092 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:27,093 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:57:27,093 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:57:27,094 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,095 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,095 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,096 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,097 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,097 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:27,098 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,098 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,099 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:57:27,100 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:57:27,100 | ^~~~~~~~~~~ 2023-09-12T10:57:27,101 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:57:27,102 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:57:27,102 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:57:27,103 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,104 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,104 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,105 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,105 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,106 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:57:27,107 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,107 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,108 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:57:27,109 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:57:27,109 | ^~~~~~~~~~~ 2023-09-12T10:57:27,110 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:57:27,111 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:57:27,112 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,113 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,114 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,115 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,115 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,116 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:57:27,117 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,118 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,119 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:57:27,119 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:57:27,120 | ^~~~~~~~~~~ 2023-09-12T10:57:27,120 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’, 2023-09-12T10:57:27,121 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,121 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,121 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,122 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,123 include/forcefields/forcefieldmmff94.h:61:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,123 61 | class OBFFTorsionCalculationMMFF94 : public OBFFCalculation4 2023-09-12T10:57:27,124 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,125 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,126 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:57:27,126 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:57:27,127 | ^~~~~~~~~~~ 2023-09-12T10:57:27,128 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’, 2023-09-12T10:57:27,128 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,129 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFTorsionCalculationMMFF94; _Args = {const OpenBabel::OBFFTorsionCalculationMMFF94&}; _Tp = OpenBabel::OBFFTorsionCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,130 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,131 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,132 include/forcefields/forcefieldmmff94.h:61:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::cosine’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,132 61 | class OBFFTorsionCalculationMMFF94 : public OBFFCalculation4 2023-09-12T10:57:27,133 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,134 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,134 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:57:27,135 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:57:27,136 | ^~~~~~~~~~~ 2023-09-12T10:57:27,136 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:27,137 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:27,138 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:57:27,138 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationMMFF94::OBFFOOPCalculationMMFF94(const OpenBabel::OBFFOOPCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:70:9, 2023-09-12T10:57:27,139 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationMMFF94; _Args = {const OpenBabel::OBFFOOPCalculationMMFF94&}; _Tp = OpenBabel::OBFFOOPCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,140 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationMMFF94; _Args = {const OpenBabel::OBFFOOPCalculationMMFF94&}; _Tp = OpenBabel::OBFFOOPCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,140 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,141 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:57:27,142 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,143 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:27,143 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,144 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,145 ./src/forcefields/forcefieldmmff94.cpp:3349:30: note: ‘oopcalc’ declared here 2023-09-12T10:57:27,146 3349 | OBFFOOPCalculationMMFF94 oopcalc; 2023-09-12T10:57:27,146 | ^~~~~~~ 2023-09-12T10:57:27,147 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:27,148 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:27,149 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:57:27,149 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationMMFF94::OBFFOOPCalculationMMFF94(const OpenBabel::OBFFOOPCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:70:9, 2023-09-12T10:57:27,150 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationMMFF94; _Args = {const OpenBabel::OBFFOOPCalculationMMFF94&}; _Tp = OpenBabel::OBFFOOPCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,151 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationMMFF94; _Args = {const OpenBabel::OBFFOOPCalculationMMFF94&}; _Tp = OpenBabel::OBFFOOPCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,152 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,153 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:57:27,153 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,154 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:27,155 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,155 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,156 ./src/forcefields/forcefieldmmff94.cpp:3349:30: note: ‘oopcalc’ declared here 2023-09-12T10:57:27,156 3349 | OBFFOOPCalculationMMFF94 oopcalc; 2023-09-12T10:57:27,157 | ^~~~~~~ 2023-09-12T10:57:27,158 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:27,158 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:57:27,159 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:57:27,160 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationMMFF94::OBFFOOPCalculationMMFF94(const OpenBabel::OBFFOOPCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:70:9, 2023-09-12T10:57:27,161 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationMMFF94; _Args = {const OpenBabel::OBFFOOPCalculationMMFF94&}; _Tp = OpenBabel::OBFFOOPCalculationMMFF94]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:27,161 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFOOPCalculationMMFF94; _Args = {const OpenBabel::OBFFOOPCalculationMMFF94&}; _Tp = OpenBabel::OBFFOOPCalculationMMFF94]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:27,162 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:27,163 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:57:27,164 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:27,165 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:27,165 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:27,166 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:57:27,167 ./src/forcefields/forcefieldmmff94.cpp:3349:30: note: ‘oopcalc’ declared here 2023-09-12T10:57:27,168 3349 | OBFFOOPCalculationMMFF94 oopcalc; 2023-09-12T10:57:27,169 | ^~~~~~~ 2023-09-12T10:57:27,169 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,170 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:57:27,170 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,171 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,172 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,172 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,173 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:57:27,174 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,174 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,175 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,176 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,177 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:57:27,177 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,178 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,179 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,180 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,181 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:57:27,181 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,182 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,183 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,184 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,185 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:57:27,186 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,186 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,187 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,188 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,189 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:57:27,189 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,190 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,190 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,191 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,192 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3426:41: 2023-09-12T10:57:27,192 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,193 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,194 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,194 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,195 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3434:41: 2023-09-12T10:57:27,196 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,197 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,198 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,198 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,199 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3599:33: 2023-09-12T10:57:27,200 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,200 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,201 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:27,202 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:57:27,202 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3661:45: 2023-09-12T10:57:27,203 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:27,203 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:27,204 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:29,813 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:57:29,813 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:29,814 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:29,814 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:30,595 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:30,595 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:30,596 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamPbci(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1262:32: 2023-09-12T10:57:30,597 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:30,597 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:30,598 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:30,599 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:30,600 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:30,600 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamPbci(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1263:32: 2023-09-12T10:57:30,601 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:30,602 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:30,603 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:30,881 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:30,881 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:30,882 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamCharge(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1230:32: 2023-09-12T10:57:30,883 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:30,883 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:30,884 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:31,171 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:31,172 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:31,173 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBndk(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:974:32: 2023-09-12T10:57:31,173 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:31,174 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:31,175 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:31,175 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:31,176 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:31,177 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBndk(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:975:32: 2023-09-12T10:57:31,177 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:31,178 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:31,178 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:31,458 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:31,459 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:31,459 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamOOP(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1117:32: 2023-09-12T10:57:31,460 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:31,461 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:31,462 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:31,743 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:31,744 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:31,744 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamDfsb(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1081:32: 2023-09-12T10:57:31,745 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:31,746 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:31,746 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:31,747 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:31,748 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:31,748 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamDfsb(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1082:32: 2023-09-12T10:57:31,749 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:31,750 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:31,751 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:32,043 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:32,044 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:32,044 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBond(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:940:32: 2023-09-12T10:57:32,045 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:32,045 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:32,045 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:32,046 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:32,046 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:32,047 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBond(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:941:32: 2023-09-12T10:57:32,047 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:32,048 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:32,048 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:32,648 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:32,649 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:32,649 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamStrBnd(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1046:32: 2023-09-12T10:57:32,650 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:32,651 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:32,652 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:32,652 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:32,653 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:32,653 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamStrBnd(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1047:32: 2023-09-12T10:57:32,654 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:32,655 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:32,655 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:32,956 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:32,957 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:32,958 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamAngle(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1010:32: 2023-09-12T10:57:32,958 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:32,959 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:32,959 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:32,960 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:32,960 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:32,961 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamAngle(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1011:32: 2023-09-12T10:57:32,961 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:32,962 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:32,962 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:33,272 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:33,273 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:33,274 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1187:32: 2023-09-12T10:57:33,274 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:33,275 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:33,276 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:33,276 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:33,277 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:33,278 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1188:32: 2023-09-12T10:57:33,278 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:33,279 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:33,279 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:33,280 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:33,281 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:33,281 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1189:32: 2023-09-12T10:57:33,282 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:33,283 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:33,283 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:33,284 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:33,284 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:33,285 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1190:32: 2023-09-12T10:57:33,285 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:33,285 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:33,286 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:33,615 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:33,615 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:33,616 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamTorsion(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1153:32: 2023-09-12T10:57:33,617 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:33,618 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:33,618 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:33,619 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:33,620 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:33,620 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamTorsion(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1154:32: 2023-09-12T10:57:33,621 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:33,622 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:33,622 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:33,623 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:33,624 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:33,624 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamTorsion(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1155:32: 2023-09-12T10:57:33,625 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:33,625 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:33,626 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,083 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’: 2023-09-12T10:57:39,083 ./src/forcefields/forcefieldmmff94.cpp:4312:15: warning: ‘eeq’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,084 4312 | snprintf(_logbuf, BUFF_SIZE, "Electrostatic %11.5f %11.5f %11.5f", E_Electrostatic(), eeq, delta); 2023-09-12T10:57:39,084 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,085 ./src/forcefields/forcefieldmmff94.cpp:3989:58: note: ‘eeq’ was declared here 2023-09-12T10:57:39,085 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,086 | ^~~ 2023-09-12T10:57:39,086 ./src/forcefields/forcefieldmmff94.cpp:4308:15: warning: ‘evdw’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,087 4308 | snprintf(_logbuf, BUFF_SIZE, "Van der Waals %11.5f %11.5f %11.5f", E_VDW(), evdw, delta); 2023-09-12T10:57:39,087 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,088 ./src/forcefields/forcefieldmmff94.cpp:3989:52: note: ‘evdw’ was declared here 2023-09-12T10:57:39,088 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,089 | ^~~~ 2023-09-12T10:57:39,089 ./src/forcefields/forcefieldmmff94.cpp:4304:15: warning: ‘etor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,090 4304 | snprintf(_logbuf, BUFF_SIZE, "Torsional %11.5f %11.5f %11.5f", E_Torsion(), etor, delta); 2023-09-12T10:57:39,090 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,091 ./src/forcefields/forcefieldmmff94.cpp:3989:46: note: ‘etor’ was declared here 2023-09-12T10:57:39,092 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,093 | ^~~~ 2023-09-12T10:57:39,093 ./src/forcefields/forcefieldmmff94.cpp:4296:15: warning: ‘estbn’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,094 4296 | snprintf(_logbuf, BUFF_SIZE, "Stretch-Bending %11.5f %11.5f %11.5f", E_StrBnd(), estbn, delta); 2023-09-12T10:57:39,095 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,095 ./src/forcefields/forcefieldmmff94.cpp:3989:39: note: ‘estbn’ was declared here 2023-09-12T10:57:39,096 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,097 | ^~~~~ 2023-09-12T10:57:39,097 ./src/forcefields/forcefieldmmff94.cpp:4300:15: warning: ‘eoop’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,098 4300 | snprintf(_logbuf, BUFF_SIZE, "Out-Of-Plane Bending %11.5f %11.5f %11.5f", E_OOP(), eoop, delta); 2023-09-12T10:57:39,098 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,099 ./src/forcefields/forcefieldmmff94.cpp:3989:33: note: ‘eoop’ was declared here 2023-09-12T10:57:39,100 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,101 | ^~~~ 2023-09-12T10:57:39,101 ./src/forcefields/forcefieldmmff94.cpp:4292:15: warning: ‘eangle’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,102 4292 | snprintf(_logbuf, BUFF_SIZE, "Angle Bending %11.5f %11.5f %11.5f", E_Angle(), eangle, delta); 2023-09-12T10:57:39,103 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,103 ./src/forcefields/forcefieldmmff94.cpp:3989:25: note: ‘eangle’ was declared here 2023-09-12T10:57:39,104 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,104 | ^~~~~~ 2023-09-12T10:57:39,105 ./src/forcefields/forcefieldmmff94.cpp:4288:15: warning: ‘ebond’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,105 4288 | snprintf(_logbuf, BUFF_SIZE, "Bond Stretching %11.5f %11.5f %11.5f", E_Bond(), ebond, delta); 2023-09-12T10:57:39,106 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,106 ./src/forcefields/forcefieldmmff94.cpp:3989:18: note: ‘ebond’ was declared here 2023-09-12T10:57:39,107 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,107 | ^~~~~ 2023-09-12T10:57:39,108 ./src/forcefields/forcefieldmmff94.cpp:4317:15: warning: ‘etot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:39,108 4317 | snprintf(_logbuf, BUFF_SIZE, "Total ENERGY %11.5f %11.5f %11.5f", Energy(), etot, delta); 2023-09-12T10:57:39,108 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,109 ./src/forcefields/forcefieldmmff94.cpp:3989:12: note: ‘etot’ was declared here 2023-09-12T10:57:39,109 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:57:39,110 | ^~~~ 2023-09-12T10:57:39,146 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,147 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,148 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4087:31: 2023-09-12T10:57:39,148 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,149 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,150 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,151 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,151 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,152 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4088:31: 2023-09-12T10:57:39,152 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,153 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,154 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,155 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,155 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,156 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4089:31: 2023-09-12T10:57:39,157 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,157 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,158 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,158 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,159 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,159 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4090:31: 2023-09-12T10:57:39,160 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,160 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,161 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,161 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,162 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,163 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4093:33: 2023-09-12T10:57:39,163 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,164 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,164 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,165 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,166 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,167 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4095:33: 2023-09-12T10:57:39,167 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,168 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,169 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,169 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,170 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,171 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4097:33: 2023-09-12T10:57:39,171 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,173 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,173 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,173 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,174 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,174 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4106:31: 2023-09-12T10:57:39,175 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,175 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,176 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,176 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,177 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,177 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4107:31: 2023-09-12T10:57:39,178 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,179 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,179 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,180 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,181 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,182 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4108:31: 2023-09-12T10:57:39,182 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,183 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,184 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,184 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,185 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,185 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4109:31: 2023-09-12T10:57:39,186 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,187 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,188 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,188 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,189 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,189 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4112:33: 2023-09-12T10:57:39,190 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,190 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,190 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,191 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,191 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,192 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4114:33: 2023-09-12T10:57:39,192 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,193 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,194 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,194 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,195 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,196 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4116:33: 2023-09-12T10:57:39,196 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,197 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,198 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:39,199 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:39,199 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:57:39,200 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4137:33: 2023-09-12T10:57:39,200 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:39,201 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:39,202 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:41,872 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:57:41,873 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmmff94.o /tmp/cctZl1MR.s 2023-09-12T10:57:41,880 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:43,611 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:57:43,612 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:57:43,612 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefieldmmff94.' 2023-09-12T10:57:43,619 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/forcefields/forcefielduff.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefielduff.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:57:43,623 Using built-in specs. 2023-09-12T10:57:43,624 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:43,625 Target: arm-linux-gnueabihf 2023-09-12T10:57:43,625 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:57:43,626 Thread model: posix 2023-09-12T10:57:43,627 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:43,627 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:43,628 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefielduff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:57:43,628 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefielduff.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/forcefields/ -dumpbase forcefielduff.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc9ToLlq.s 2023-09-12T10:57:43,637 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:43,638 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:43,638 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:43,639 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:43,639 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:43,640 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:43,640 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:43,641 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:43,641 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:43,642 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:43,642 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:43,643 #include "..." search starts here: 2023-09-12T10:57:43,643 #include <...> search starts here: 2023-09-12T10:57:43,644 /usr/include/eigen3 2023-09-12T10:57:43,645 include 2023-09-12T10:57:43,645 /usr/include/python3.11 2023-09-12T10:57:43,646 /usr/include/c++/12 2023-09-12T10:57:43,647 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:43,647 /usr/include/c++/12/backward 2023-09-12T10:57:43,648 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:43,648 /usr/local/include 2023-09-12T10:57:43,649 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:43,650 /usr/include 2023-09-12T10:57:43,650 End of search list. 2023-09-12T10:57:43,651 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:43,652 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:43,653 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:43,653 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:43,660 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:45,241 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:45,241 from include/openbabel/mol.h:43, 2023-09-12T10:57:45,242 from ./src/forcefields/forcefielduff.cpp:21: 2023-09-12T10:57:45,243 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:45,243 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:45,244 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:45,245 | ^ 2023-09-12T10:57:45,246 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:45,247 37 | # define UNUSED(x) x 2023-09-12T10:57:45,247 | ^ 2023-09-12T10:57:46,011 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:46,012 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:46,013 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:46,014 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:46,015 | ^ 2023-09-12T10:57:46,016 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:46,017 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:46,018 | ^~~~~~~~ 2023-09-12T10:57:46,019 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:46,020 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:46,021 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:46,022 | ^ 2023-09-12T10:57:46,023 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:46,024 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:46,025 | ^~~~~~~~ 2023-09-12T10:57:46,037 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:46,037 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:46,038 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:46,039 | ^ 2023-09-12T10:57:46,040 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:46,040 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:46,041 | ^~~~~~~~ 2023-09-12T10:57:46,043 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:46,044 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:46,045 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:46,045 | ^ 2023-09-12T10:57:46,046 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:46,047 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:46,047 | ^~~~~~~~ 2023-09-12T10:57:46,358 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:57:46,358 from include/forcefields/forcefielduff.h:24, 2023-09-12T10:57:46,359 from ./src/forcefields/forcefielduff.cpp:24: 2023-09-12T10:57:46,360 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:46,360 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:46,361 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:46,361 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:46,362 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:46,363 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:46,363 from include/openbabel/mol.h:35: 2023-09-12T10:57:46,364 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:46,364 131 | struct binary_function 2023-09-12T10:57:46,365 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:46,486 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:57:46,486 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,487 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,488 | ^ 2023-09-12T10:57:46,488 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,489 37 | # define UNUSED(x) x 2023-09-12T10:57:46,490 | ^ 2023-09-12T10:57:46,490 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:57:46,491 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,492 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,493 | ^ 2023-09-12T10:57:46,493 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,494 37 | # define UNUSED(x) x 2023-09-12T10:57:46,495 | ^ 2023-09-12T10:57:46,496 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:57:46,497 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,497 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,498 | ^ 2023-09-12T10:57:46,499 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,500 37 | # define UNUSED(x) x 2023-09-12T10:57:46,500 | ^ 2023-09-12T10:57:46,501 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:57:46,502 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,502 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,503 | ^ 2023-09-12T10:57:46,504 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,504 37 | # define UNUSED(x) x 2023-09-12T10:57:46,505 | ^ 2023-09-12T10:57:46,506 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:57:46,507 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,507 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,508 | ^ 2023-09-12T10:57:46,509 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,509 37 | # define UNUSED(x) x 2023-09-12T10:57:46,510 | ^ 2023-09-12T10:57:46,510 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:57:46,511 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,511 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,512 | ^ 2023-09-12T10:57:46,512 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,513 37 | # define UNUSED(x) x 2023-09-12T10:57:46,513 | ^ 2023-09-12T10:57:46,514 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:57:46,514 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,515 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,515 | ^ 2023-09-12T10:57:46,516 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,516 37 | # define UNUSED(x) x 2023-09-12T10:57:46,517 | ^ 2023-09-12T10:57:46,518 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:57:46,518 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:57:46,519 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:57:46,520 | ^ 2023-09-12T10:57:46,521 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:46,521 37 | # define UNUSED(x) x 2023-09-12T10:57:46,522 | ^ 2023-09-12T10:57:47,451 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = true]’: 2023-09-12T10:57:47,452 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = true]’ 2023-09-12T10:57:47,453 include/forcefields/forcefielduff.h:192:37: required from here 2023-09-12T10:57:47,454 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-12T10:57:47,454 423 | double ab[3]; 2023-09-12T10:57:47,455 | ^~ 2023-09-12T10:57:47,456 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = false]’: 2023-09-12T10:57:47,456 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = false]’ 2023-09-12T10:57:47,457 include/forcefields/forcefielduff.h:192:54: required from here 2023-09-12T10:57:47,458 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-12T10:57:54,495 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:57:54,496 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’: 2023-09-12T10:57:54,497 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:54,498 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:54,499 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:54,643 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFVDWCalculationUFF&}; _Tp = OpenBabel::OBFFVDWCalculationUFF; _Alloc = std::allocator]’: 2023-09-12T10:57:54,644 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:54,827 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’: 2023-09-12T10:57:54,827 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:55,086 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFTorsionCalculationUFF&}; _Tp = OpenBabel::OBFFTorsionCalculationUFF; _Alloc = std::allocator]’: 2023-09-12T10:57:55,086 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:55,325 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFOOPCalculationUFF&}; _Tp = OpenBabel::OBFFOOPCalculationUFF; _Alloc = std::allocator]’: 2023-09-12T10:57:55,325 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:56,563 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:56,563 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2023-09-12T10:57:56,564 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:56,565 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:56,566 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:56,566 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:57:56,567 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:56,568 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:56,568 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:56,569 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:57:56,570 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:57:56,571 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:57:56,572 | ^~~~~~~~ 2023-09-12T10:57:56,572 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:56,573 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2023-09-12T10:57:56,573 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:56,574 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:56,574 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:56,575 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:57:56,575 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:56,576 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:56,577 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:56,577 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:57:56,578 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:57:56,579 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:57:56,580 | ^~~~~~~~ 2023-09-12T10:57:56,581 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:56,582 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2023-09-12T10:57:56,583 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:56,584 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:56,584 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:56,585 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:57:56,586 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:56,587 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:56,588 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:56,588 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:57:56,589 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:57:56,589 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:57:56,590 | ^~~~~~~~ 2023-09-12T10:57:56,590 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2023-09-12T10:57:56,591 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:56,592 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:56,592 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:56,593 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:57:56,594 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:56,594 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2023-09-12T10:57:56,595 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:56,596 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:57:56,597 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:57:56,598 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:57:56,598 | ^~~~~~~~ 2023-09-12T10:57:56,599 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2023-09-12T10:57:56,600 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:56,601 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationUFF; _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:56,602 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:56,602 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:57:56,603 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:56,604 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2023-09-12T10:57:56,604 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:56,605 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:57:56,606 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:57:56,607 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:57:56,607 | ^~~~~~~~ 2023-09-12T10:57:56,648 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:57:56,648 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,649 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:57:56,649 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,650 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,651 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:56,655 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,655 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:979:37: 2023-09-12T10:57:56,656 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,656 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,657 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:56,659 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,659 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2023-09-12T10:57:56,660 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,661 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,662 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:56,667 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,668 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1273:37: 2023-09-12T10:57:56,668 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,669 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,670 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:56,673 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,674 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1395:33: 2023-09-12T10:57:56,674 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,675 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,676 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:56,677 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,677 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1402:33: 2023-09-12T10:57:56,678 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,678 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,679 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:56,679 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,680 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1410:33: 2023-09-12T10:57:56,680 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,681 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,681 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:56,682 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:56,683 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1454:35: 2023-09-12T10:57:56,684 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:56,684 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:56,685 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:57:59,695 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’: 2023-09-12T10:57:59,695 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:59,696 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:59,696 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:59,866 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:59,867 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2023-09-12T10:57:59,868 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:59,868 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:59,869 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:59,870 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:57:59,871 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:59,871 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:59,872 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:59,872 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:57:59,873 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:57:59,874 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:57:59,874 | ^~~~~~~ 2023-09-12T10:57:59,875 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:59,875 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2023-09-12T10:57:59,876 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:59,876 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:59,877 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:59,878 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:57:59,879 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:59,879 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:59,880 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:59,881 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:57:59,881 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:57:59,882 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:57:59,882 | ^~~~~~~ 2023-09-12T10:57:59,883 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:57:59,884 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2023-09-12T10:57:59,885 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:59,886 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:59,886 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:59,887 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:57:59,887 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:59,888 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:57:59,888 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:57:59,889 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:57:59,889 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:57:59,890 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:57:59,890 | ^~~~~~~ 2023-09-12T10:57:59,891 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’, 2023-09-12T10:57:59,892 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/new_allocator.h:175:4, 2023-09-12T10:57:59,893 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationUFF; _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, 2023-09-12T10:57:59,893 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, 2023-09-12T10:57:59,894 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:57:59,895 include/forcefields/forcefielduff.h:82:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:57:59,895 82 | class OBFFElectrostaticCalculationUFF : public OBFFCalculation2 2023-09-12T10:57:59,896 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:59,897 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:57:59,897 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:57:59,898 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:57:59,898 | ^~~~~~~ 2023-09-12T10:57:59,899 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:57:59,900 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:57:59,901 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:57:59,901 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:57:59,902 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:58:00,157 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:58:00,158 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:58:00,158 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:58:00,159 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,434 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,435 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,436 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1576:34: 2023-09-12T10:58:03,436 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,437 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,438 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,439 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,439 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,440 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1577:34: 2023-09-12T10:58:03,441 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,442 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,443 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,443 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,444 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,444 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1578:34: 2023-09-12T10:58:03,445 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,446 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,447 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,448 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,449 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,449 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1579:34: 2023-09-12T10:58:03,450 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,451 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,451 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,452 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,453 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,453 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1580:34: 2023-09-12T10:58:03,454 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,454 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,455 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,456 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,456 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,457 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1581:34: 2023-09-12T10:58:03,458 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,459 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,460 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,461 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,461 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,462 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1582:34: 2023-09-12T10:58:03,463 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,463 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,464 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,465 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,466 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,466 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1583:34: 2023-09-12T10:58:03,467 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,468 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,468 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,469 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,469 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,470 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1584:34: 2023-09-12T10:58:03,470 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,471 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,471 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,472 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,472 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,473 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1585:34: 2023-09-12T10:58:03,473 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,474 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,475 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:03,476 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:58:03,477 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:58:03,477 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1586:34: 2023-09-12T10:58:03,478 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:58:03,479 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:58:03,479 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:05,978 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefielduff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/' 2023-09-12T10:58:05,979 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefielduff.o /tmp/cc9ToLlq.s 2023-09-12T10:58:05,984 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:07,137 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:58:07,137 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:58:07,138 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefielduff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefielduff.' 2023-09-12T10:58:07,143 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/format.cpp -o build/temp.linux-armv7l-cpython-311/./src/format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:07,148 Using built-in specs. 2023-09-12T10:58:07,148 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:07,149 Target: arm-linux-gnueabihf 2023-09-12T10:58:07,150 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:58:07,150 Thread model: posix 2023-09-12T10:58:07,151 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:07,152 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:07,152 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:58:07,153 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/format.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/ -dumpbase format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccxILYSg.s 2023-09-12T10:58:07,162 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:07,163 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:07,165 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:07,165 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:07,166 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:07,166 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:07,167 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:07,167 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:07,168 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:07,168 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:07,169 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:07,170 #include "..." search starts here: 2023-09-12T10:58:07,170 #include <...> search starts here: 2023-09-12T10:58:07,171 /usr/include/eigen3 2023-09-12T10:58:07,172 include 2023-09-12T10:58:07,172 /usr/include/python3.11 2023-09-12T10:58:07,173 /usr/include/c++/12 2023-09-12T10:58:07,174 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:07,174 /usr/include/c++/12/backward 2023-09-12T10:58:07,175 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:07,175 /usr/local/include 2023-09-12T10:58:07,176 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:07,177 /usr/include 2023-09-12T10:58:07,177 End of search list. 2023-09-12T10:58:07,178 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:07,179 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:07,180 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:07,181 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:07,182 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:09,448 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:09,553 from ./src/format.cpp:20: 2023-09-12T10:58:09,561 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:09,627 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:09,661 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:09,662 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:58:09,663 from include/openbabel/plugin.h:23: 2023-09-12T10:58:09,664 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:09,669 131 | struct binary_function 2023-09-12T10:58:09,670 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:10,939 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/' 2023-09-12T10:58:10,940 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/format.o /tmp/ccxILYSg.s 2023-09-12T10:58:10,945 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:11,045 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:58:11,045 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:58:11,046 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/format.' 2023-09-12T10:58:11,047 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/APIInterface.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/APIInterface.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:11,051 Using built-in specs. 2023-09-12T10:58:11,052 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:11,052 Target: arm-linux-gnueabihf 2023-09-12T10:58:11,053 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:58:11,053 Thread model: posix 2023-09-12T10:58:11,054 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:11,054 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:11,055 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/APIInterface.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:11,056 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/APIInterface.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase APIInterface.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc8frAme.s 2023-09-12T10:58:11,064 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:11,065 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:11,066 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:11,067 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:11,067 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:11,067 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:11,068 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:11,068 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:11,069 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:11,069 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:11,070 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:11,070 #include "..." search starts here: 2023-09-12T10:58:11,071 #include <...> search starts here: 2023-09-12T10:58:11,071 /usr/include/eigen3 2023-09-12T10:58:11,072 include 2023-09-12T10:58:11,072 /usr/include/python3.11 2023-09-12T10:58:11,073 /usr/include/c++/12 2023-09-12T10:58:11,073 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:11,074 /usr/include/c++/12/backward 2023-09-12T10:58:11,074 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:11,075 /usr/local/include 2023-09-12T10:58:11,075 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:11,076 /usr/include 2023-09-12T10:58:11,076 End of search list. 2023-09-12T10:58:11,077 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:11,078 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:11,079 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:11,079 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:11,083 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:12,505 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:12,505 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:12,506 from ./src/formats/APIInterface.cpp:19: 2023-09-12T10:58:12,507 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:12,507 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:12,508 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:12,511 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:58:12,511 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:58:12,512 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:58:12,513 from /usr/include/c++/12/ios:42, 2023-09-12T10:58:12,514 from /usr/include/c++/12/ostream:38, 2023-09-12T10:58:12,514 from /usr/include/c++/12/iostream:39, 2023-09-12T10:58:12,515 from include/openbabel/obconversion.h:24: 2023-09-12T10:58:12,516 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:12,516 131 | struct binary_function 2023-09-12T10:58:12,517 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:13,559 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/APIInterface.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:13,560 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/APIInterface.o /tmp/cc8frAme.s 2023-09-12T10:58:13,566 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:13,652 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:58:13,654 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:58:13,655 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/APIInterface.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/APIInterface.' 2023-09-12T10:58:13,656 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/ArrayList.c -o build/temp.linux-armv7l-cpython-311/./src/formats/ArrayList.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:13,664 Using built-in specs. 2023-09-12T10:58:13,665 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:13,665 Target: arm-linux-gnueabihf 2023-09-12T10:58:13,666 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:58:13,666 Thread model: posix 2023-09-12T10:58:13,667 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:13,668 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:13,668 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/ArrayList.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:13,668 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1 -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D NDEBUG ./src/formats/ArrayList.c -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase ArrayList.c -dumpbase-ext .c -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc6u2lJr.s 2023-09-12T10:58:13,678 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 2023-09-12T10:58:13,678 GNU C17 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:13,679 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:13,680 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:13,680 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:13,681 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:13,681 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:13,682 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:13,683 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:13,683 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:13,684 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:13,685 #include "..." search starts here: 2023-09-12T10:58:13,686 #include <...> search starts here: 2023-09-12T10:58:13,686 /usr/include/eigen3 2023-09-12T10:58:13,687 include 2023-09-12T10:58:13,687 /usr/include/python3.11 2023-09-12T10:58:13,688 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:13,689 /usr/local/include 2023-09-12T10:58:13,689 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:13,690 /usr/include 2023-09-12T10:58:13,690 End of search list. 2023-09-12T10:58:13,691 GNU C17 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:13,691 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:13,692 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:13,693 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:13,694 Compiler executable checksum: aa6629b5f44fe3420ba005fbae7bc0e6 2023-09-12T10:58:13,909 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/ArrayList.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:13,910 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/ArrayList.o /tmp/cc6u2lJr.s 2023-09-12T10:58:13,915 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:13,924 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:58:13,925 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:58:13,925 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/ArrayList.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/ArrayList.' 2023-09-12T10:58:13,926 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/CSRformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/CSRformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:13,930 Using built-in specs. 2023-09-12T10:58:13,930 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:13,931 Target: arm-linux-gnueabihf 2023-09-12T10:58:13,931 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:58:13,932 Thread model: posix 2023-09-12T10:58:13,933 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:13,933 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:13,934 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/CSRformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:13,934 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/CSRformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase CSRformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc70LX0j.s 2023-09-12T10:58:13,943 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:13,944 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:13,945 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:13,945 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:13,946 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:13,946 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:13,946 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:13,947 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:13,947 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:13,948 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:13,948 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:13,948 #include "..." search starts here: 2023-09-12T10:58:13,949 #include <...> search starts here: 2023-09-12T10:58:13,950 /usr/include/eigen3 2023-09-12T10:58:13,950 include 2023-09-12T10:58:13,951 /usr/include/python3.11 2023-09-12T10:58:13,951 /usr/include/c++/12 2023-09-12T10:58:13,952 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:13,953 /usr/include/c++/12/backward 2023-09-12T10:58:13,953 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:13,954 /usr/local/include 2023-09-12T10:58:13,955 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:13,955 /usr/include 2023-09-12T10:58:13,956 End of search list. 2023-09-12T10:58:13,957 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:13,957 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:13,958 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:13,959 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:13,962 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:15,538 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:15,538 from include/openbabel/mol.h:43, 2023-09-12T10:58:15,539 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:15,539 from ./src/formats/CSRformat.cpp:17: 2023-09-12T10:58:15,540 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:15,541 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:15,541 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:15,542 | ^ 2023-09-12T10:58:15,543 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:15,543 37 | # define UNUSED(x) x 2023-09-12T10:58:15,544 | ^ 2023-09-12T10:58:16,319 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:16,320 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:16,321 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:16,322 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:16,323 | ^ 2023-09-12T10:58:16,323 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:16,324 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:16,324 | ^~~~~~~~ 2023-09-12T10:58:16,325 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:16,326 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:16,326 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:16,327 | ^ 2023-09-12T10:58:16,328 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:16,328 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:16,329 | ^~~~~~~~ 2023-09-12T10:58:16,345 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:16,345 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:16,346 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:16,347 | ^ 2023-09-12T10:58:16,347 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:16,348 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:16,349 | ^~~~~~~~ 2023-09-12T10:58:16,351 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:16,352 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:16,353 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:16,354 | ^ 2023-09-12T10:58:16,354 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:16,355 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:16,356 | ^~~~~~~~ 2023-09-12T10:58:16,526 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:16,526 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:16,527 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:16,528 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:16,528 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:16,529 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:16,530 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:16,531 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:16,531 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:16,532 from include/openbabel/mol.h:35: 2023-09-12T10:58:16,532 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:16,533 131 | struct binary_function 2023-09-12T10:58:16,533 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:18,756 ./src/formats/CSRformat.cpp: In member function ‘char* OpenBabel::CSRFormat::PadString(char*, int)’: 2023-09-12T10:58:18,756 ./src/formats/CSRformat.cpp:188:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2023-09-12T10:58:18,757 188 | strncpy(output, input, strlen(input)); 2023-09-12T10:58:18,757 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:18,963 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/CSRformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:18,964 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/CSRformat.o /tmp/cc70LX0j.s 2023-09-12T10:58:18,968 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:19,101 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:58:19,102 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:58:19,102 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/CSRformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/CSRformat.' 2023-09-12T10:58:19,103 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/MCDLformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/MCDLformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:19,107 Using built-in specs. 2023-09-12T10:58:19,108 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:19,109 Target: arm-linux-gnueabihf 2023-09-12T10:58:19,110 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:58:19,110 Thread model: posix 2023-09-12T10:58:19,111 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:19,111 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:19,112 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/MCDLformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:19,112 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/MCDLformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase MCDLformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccbNUqft.s 2023-09-12T10:58:19,121 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:19,122 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:19,123 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:19,123 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:19,124 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:19,124 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:19,125 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:19,126 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:19,126 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:19,127 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:19,127 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:19,128 #include "..." search starts here: 2023-09-12T10:58:19,128 #include <...> search starts here: 2023-09-12T10:58:19,129 /usr/include/eigen3 2023-09-12T10:58:19,129 include 2023-09-12T10:58:19,130 /usr/include/python3.11 2023-09-12T10:58:19,131 /usr/include/c++/12 2023-09-12T10:58:19,131 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:19,132 /usr/include/c++/12/backward 2023-09-12T10:58:19,132 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:19,133 /usr/local/include 2023-09-12T10:58:19,134 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:19,134 /usr/include 2023-09-12T10:58:19,135 End of search list. 2023-09-12T10:58:19,136 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:19,136 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:19,137 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:19,138 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:19,139 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:20,709 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:20,709 from include/openbabel/mol.h:43, 2023-09-12T10:58:20,710 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:20,710 from ./src/formats/MCDLformat.cpp:21: 2023-09-12T10:58:20,711 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:20,711 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:20,712 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:20,713 | ^ 2023-09-12T10:58:20,713 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:20,714 37 | # define UNUSED(x) x 2023-09-12T10:58:20,714 | ^ 2023-09-12T10:58:21,479 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:21,480 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:21,480 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:21,481 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:21,482 | ^ 2023-09-12T10:58:21,482 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:21,483 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:21,484 | ^~~~~~~~ 2023-09-12T10:58:21,486 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:21,486 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:21,487 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:21,488 | ^ 2023-09-12T10:58:21,488 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:21,489 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:21,490 | ^~~~~~~~ 2023-09-12T10:58:21,506 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:21,506 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:21,507 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:21,508 | ^ 2023-09-12T10:58:21,508 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:21,509 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:21,510 | ^~~~~~~~ 2023-09-12T10:58:21,513 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:21,514 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:21,514 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:21,515 | ^ 2023-09-12T10:58:21,515 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:21,516 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:21,517 | ^~~~~~~~ 2023-09-12T10:58:21,687 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:21,687 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:21,688 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:21,688 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:21,689 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:21,689 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:21,690 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:21,691 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:21,691 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:21,692 from include/openbabel/mol.h:35: 2023-09-12T10:58:21,693 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:21,693 131 | struct binary_function 2023-09-12T10:58:21,694 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:21,902 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::constring(int (*)[4], char*)’: 2023-09-12T10:58:21,903 ./src/formats/MCDLformat.cpp:174:66: warning: unused parameter ‘tstr’ [-Wunused-parameter] 2023-09-12T10:58:21,903 174 | string MCDLFormat::constring(int conntab [MAXBONDS][4], char * tstr) 2023-09-12T10:58:21,904 | ~~~~~~~^~~~ 2023-09-12T10:58:21,906 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2023-09-12T10:58:21,906 ./src/formats/MCDLformat.cpp:278:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:58:21,907 278 | if (jflag) 2023-09-12T10:58:21,907 | ^~ 2023-09-12T10:58:21,908 ./src/formats/MCDLformat.cpp:282:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T10:58:21,909 282 | nt = 1; 2023-09-12T10:58:21,909 | ^~ 2023-09-12T10:58:21,957 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::getMCDL(OpenBabel::OBMol*, bool)’: 2023-09-12T10:58:21,958 ./src/formats/MCDLformat.cpp:529:10: warning: variable ‘test’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:58:21,959 529 | bool test;//, testParity; 2023-09-12T10:58:21,959 | ^~~~ 2023-09-12T10:58:21,962 ./src/formats/MCDLformat.cpp:479:48: warning: unused parameter ‘includeCoordinates’ [-Wunused-parameter] 2023-09-12T10:58:21,963 479 | string MCDLFormat::getMCDL(OBMol* pmol, bool includeCoordinates) { 2023-09-12T10:58:21,964 | ~~~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:21,965 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::restoreFullMCDL(std::string, OpenBabel::OBMol*)’: 2023-09-12T10:58:21,965 ./src/formats/MCDLformat.cpp:948:43: warning: unused parameter ‘value’ [-Wunused-parameter] 2023-09-12T10:58:21,966 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2023-09-12T10:58:21,966 | ~~~~~~~^~~~~ 2023-09-12T10:58:21,967 ./src/formats/MCDLformat.cpp:948:57: warning: unused parameter ‘pmol’ [-Wunused-parameter] 2023-09-12T10:58:21,967 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2023-09-12T10:58:21,968 | ~~~~~~~^~~~ 2023-09-12T10:58:21,977 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::setMCDL(std::string, OpenBabel::OBMol*, std::string&)’: 2023-09-12T10:58:21,978 ./src/formats/MCDLformat.cpp:1031:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:58:21,978 1031 | if (n1 < 0) n1=indexOf(s,"-"); 2023-09-12T10:58:21,979 | ~~~^~~ 2023-09-12T10:58:21,979 ./src/formats/MCDLformat.cpp:1032:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:58:21,980 1032 | if (n1 < 0) n1=indexOf(s,"*"); 2023-09-12T10:58:21,981 | ~~~^~~ 2023-09-12T10:58:21,981 ./src/formats/MCDLformat.cpp:1033:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:58:21,982 1033 | if (n1 < 0) { 2023-09-12T10:58:21,983 | ~~~^~~ 2023-09-12T10:58:21,983 ./src/formats/MCDLformat.cpp:1062:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:21,984 1062 | if (n1>=0) { 2023-09-12T10:58:21,985 | ~~^~~ 2023-09-12T10:58:21,986 ./src/formats/MCDLformat.cpp:1070:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:21,987 1070 | if (n1>=0) { 2023-09-12T10:58:21,987 | ~~^~~ 2023-09-12T10:58:21,989 ./src/formats/MCDLformat.cpp:1079:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:21,989 1079 | if (n1>=0) { 2023-09-12T10:58:21,990 | ~~^~~ 2023-09-12T10:58:21,993 ./src/formats/MCDLformat.cpp:1092:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:21,994 1092 | if (n1>=0) { 2023-09-12T10:58:21,994 | ~~^~~ 2023-09-12T10:58:21,997 ./src/formats/MCDLformat.cpp:1118:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:58:21,998 1118 | if (n1<0) { 2023-09-12T10:58:21,999 | ~~^~ 2023-09-12T10:58:21,999 ./src/formats/MCDLformat.cpp:1121:25: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:22,000 1121 | if ((n2=0)) n1=n2; 2023-09-12T10:58:22,001 | ~~^~~ 2023-09-12T10:58:22,014 ./src/formats/MCDLformat.cpp:1266:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:58:22,014 1266 | if (nPrev == acount) { 2023-09-12T10:58:22,015 | ~~~~~~^~~~~~~~~ 2023-09-12T10:58:22,017 ./src/formats/MCDLformat.cpp:1298:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:58:22,018 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2023-09-12T10:58:22,019 | ~~^~ 2023-09-12T10:58:22,020 ./src/formats/MCDLformat.cpp:1298:45: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:22,020 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2023-09-12T10:58:22,021 | ~~^~~ 2023-09-12T10:58:22,021 ./src/formats/MCDLformat.cpp:1300:12: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:22,022 1300 | if ((n1>=0) && (value.length() > n1)) { 2023-09-12T10:58:22,022 | ~~^~~ 2023-09-12T10:58:22,023 ./src/formats/MCDLformat.cpp:1312:13: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:22,023 1312 | if (n1>=0) { 2023-09-12T10:58:22,024 | ~~^~~ 2023-09-12T10:58:22,034 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::indexOf(std::string, std::string, int)’: 2023-09-12T10:58:22,035 ./src/formats/MCDLformat.cpp:1384:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2023-09-12T10:58:22,035 1384 | if (result == string::npos) result=-1; 2023-09-12T10:58:22,036 | ~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T10:58:22,036 ./src/formats/MCDLformat.cpp:1385:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:58:22,037 1385 | if (result >= instring.length()) result=-1; 2023-09-12T10:58:22,037 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:22,038 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::lastIndexOf(std::string, std::string)’: 2023-09-12T10:58:22,039 ./src/formats/MCDLformat.cpp:1398:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2023-09-12T10:58:22,039 1398 | if (n == string::npos) 2023-09-12T10:58:22,040 | ~~^~~~~~~~~~~~~~~ 2023-09-12T10:58:22,041 ./src/formats/MCDLformat.cpp: In member function ‘bool OpenBabel::MCDLFormat::parseFormula(std::string, std::vector&)’: 2023-09-12T10:58:22,041 ./src/formats/MCDLformat.cpp:1426:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:22,042 1426 | if (n>=0) { 2023-09-12T10:58:22,043 | ~^~~ 2023-09-12T10:58:22,045 ./src/formats/MCDLformat.cpp:1449:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:58:22,045 1449 | if (n>=0) { 2023-09-12T10:58:22,046 | ~^~~ 2023-09-12T10:58:26,467 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2023-09-12T10:58:26,467 ./src/formats/MCDLformat.cpp:237:28: warning: ‘jump’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:26,468 237 | int numdups, dupfrag, jump; 2023-09-12T10:58:26,469 | ^~~~ 2023-09-12T10:58:26,470 ./src/formats/MCDLformat.cpp:395:22: warning: ‘dupfrag’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:26,470 395 | else if (ix[i] == dupfrag && j != dupnum) 2023-09-12T10:58:26,471 | ^~ 2023-09-12T10:58:26,472 ./src/formats/MCDLformat.cpp:237:19: note: ‘dupfrag’ was declared here 2023-09-12T10:58:26,472 237 | int numdups, dupfrag, jump; 2023-09-12T10:58:26,473 | ^~~~~~~ 2023-09-12T10:58:26,474 ./src/formats/MCDLformat.cpp:385:24: warning: ‘numdups’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:26,475 385 | for (j=0; j search starts here: 2023-09-12T10:58:44,155 /usr/include/eigen3 2023-09-12T10:58:44,155 include 2023-09-12T10:58:44,156 /usr/include/python3.11 2023-09-12T10:58:44,156 /usr/include/c++/12 2023-09-12T10:58:44,157 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:44,157 /usr/include/c++/12/backward 2023-09-12T10:58:44,158 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:44,158 /usr/local/include 2023-09-12T10:58:44,159 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:44,159 /usr/include 2023-09-12T10:58:44,160 End of search list. 2023-09-12T10:58:44,161 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:44,161 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:44,162 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:44,163 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:44,169 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:45,738 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:45,739 from include/openbabel/mol.h:43, 2023-09-12T10:58:45,740 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:45,741 from ./src/formats/MNAformat.cpp:31: 2023-09-12T10:58:45,741 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:45,742 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:45,743 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:45,744 | ^ 2023-09-12T10:58:45,744 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:45,745 37 | # define UNUSED(x) x 2023-09-12T10:58:45,745 | ^ 2023-09-12T10:58:46,509 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:46,509 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:46,510 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:46,511 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:46,511 | ^ 2023-09-12T10:58:46,512 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:46,512 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:46,513 | ^~~~~~~~ 2023-09-12T10:58:46,514 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:46,515 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:46,515 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:46,516 | ^ 2023-09-12T10:58:46,517 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:46,518 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:46,518 | ^~~~~~~~ 2023-09-12T10:58:46,533 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:46,534 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:46,535 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:46,535 | ^ 2023-09-12T10:58:46,536 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:46,537 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:46,537 | ^~~~~~~~ 2023-09-12T10:58:46,540 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:46,540 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:46,541 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:46,542 | ^ 2023-09-12T10:58:46,543 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:46,543 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:46,544 | ^~~~~~~~ 2023-09-12T10:58:46,713 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:46,714 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:46,714 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:46,715 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:46,715 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:46,716 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:46,716 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:46,717 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:46,717 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:46,718 from include/openbabel/mol.h:35: 2023-09-12T10:58:46,718 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:46,719 131 | struct binary_function 2023-09-12T10:58:46,720 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:50,941 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/MNAformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:50,942 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/MNAformat.o /tmp/cc2plojT.s 2023-09-12T10:58:50,946 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:51,248 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:58:51,249 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:58:51,250 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/MNAformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/MNAformat.' 2023-09-12T10:58:51,250 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/PQSformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/PQSformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:51,254 Using built-in specs. 2023-09-12T10:58:51,255 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:51,255 Target: arm-linux-gnueabihf 2023-09-12T10:58:51,256 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:58:51,256 Thread model: posix 2023-09-12T10:58:51,257 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:51,257 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:51,258 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/PQSformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:51,258 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/PQSformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase PQSformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccMIuUj7.s 2023-09-12T10:58:51,267 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:51,268 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:51,269 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:51,269 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:51,270 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:51,270 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:51,271 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:51,271 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:51,272 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:51,273 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:51,273 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:51,274 #include "..." search starts here: 2023-09-12T10:58:51,274 #include <...> search starts here: 2023-09-12T10:58:51,275 /usr/include/eigen3 2023-09-12T10:58:51,276 include 2023-09-12T10:58:51,276 /usr/include/python3.11 2023-09-12T10:58:51,277 /usr/include/c++/12 2023-09-12T10:58:51,278 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:51,278 /usr/include/c++/12/backward 2023-09-12T10:58:51,279 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:51,279 /usr/local/include 2023-09-12T10:58:51,280 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:51,280 /usr/include 2023-09-12T10:58:51,281 End of search list. 2023-09-12T10:58:51,281 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:51,282 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:51,282 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:51,283 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:51,286 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:52,878 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:52,879 from include/openbabel/mol.h:43, 2023-09-12T10:58:52,880 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:52,881 from ./src/formats/PQSformat.cpp:16: 2023-09-12T10:58:52,881 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:52,882 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:52,883 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:52,883 | ^ 2023-09-12T10:58:52,884 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:52,885 37 | # define UNUSED(x) x 2023-09-12T10:58:52,886 | ^ 2023-09-12T10:58:53,659 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:53,660 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:53,660 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:53,661 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:53,662 | ^ 2023-09-12T10:58:53,663 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:53,663 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:53,664 | ^~~~~~~~ 2023-09-12T10:58:53,666 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:53,666 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:53,667 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:53,668 | ^ 2023-09-12T10:58:53,668 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:53,669 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:53,670 | ^~~~~~~~ 2023-09-12T10:58:53,686 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:53,687 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:53,687 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:53,688 | ^ 2023-09-12T10:58:53,689 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:53,690 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:53,690 | ^~~~~~~~ 2023-09-12T10:58:53,693 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:53,693 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:53,694 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:53,695 | ^ 2023-09-12T10:58:53,695 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:53,696 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:53,696 | ^~~~~~~~ 2023-09-12T10:58:53,866 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:53,867 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:53,868 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:53,868 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:53,869 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:53,870 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:53,870 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:53,871 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:53,872 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:53,873 from include/openbabel/mol.h:35: 2023-09-12T10:58:53,873 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:53,874 131 | struct binary_function 2023-09-12T10:58:53,875 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:56,760 ./src/formats/PQSformat.cpp: In member function ‘virtual bool OpenBabel::PQSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:58:56,761 ./src/formats/PQSformat.cpp:259:49: warning: ‘pFormat’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:56,761 259 | return pFormat->ReadMolecule(&mol,&coordconv); 2023-09-12T10:58:56,762 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:58:56,763 ./src/formats/PQSformat.cpp:250:31: note: ‘pFormat’ was declared here 2023-09-12T10:58:56,764 250 | OBFormat* pFormat; 2023-09-12T10:58:56,764 | ^~~~~~~ 2023-09-12T10:58:57,444 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/PQSformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:57,445 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/PQSformat.o /tmp/ccMIuUj7.s 2023-09-12T10:58:57,449 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:57,674 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:58:57,675 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:58:57,675 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/PQSformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/PQSformat.' 2023-09-12T10:58:57,676 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/abinitformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/abinitformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:57,680 Using built-in specs. 2023-09-12T10:58:57,681 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:57,682 Target: arm-linux-gnueabihf 2023-09-12T10:58:57,682 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:58:57,683 Thread model: posix 2023-09-12T10:58:57,683 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:57,684 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:57,685 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/abinitformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:58:57,685 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/abinitformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase abinitformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cch18f2d.s 2023-09-12T10:58:57,694 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:57,695 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:57,696 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:57,696 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:57,697 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:57,697 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:57,698 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:57,698 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:57,699 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:57,699 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:57,700 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:57,700 #include "..." search starts here: 2023-09-12T10:58:57,701 #include <...> search starts here: 2023-09-12T10:58:57,702 /usr/include/eigen3 2023-09-12T10:58:57,703 include 2023-09-12T10:58:57,704 /usr/include/python3.11 2023-09-12T10:58:57,704 /usr/include/c++/12 2023-09-12T10:58:57,705 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:57,706 /usr/include/c++/12/backward 2023-09-12T10:58:57,706 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:57,707 /usr/local/include 2023-09-12T10:58:57,708 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:57,708 /usr/include 2023-09-12T10:58:57,709 End of search list. 2023-09-12T10:58:57,709 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:57,710 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:57,711 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:57,712 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:57,713 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:59,304 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:59,304 from include/openbabel/mol.h:43, 2023-09-12T10:58:59,305 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:59,306 from ./src/formats/abinitformat.cpp:16: 2023-09-12T10:58:59,306 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:59,307 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:59,307 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:59,308 | ^ 2023-09-12T10:58:59,309 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:59,309 37 | # define UNUSED(x) x 2023-09-12T10:58:59,310 | ^ 2023-09-12T10:59:00,074 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:00,075 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:00,076 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:00,077 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:00,077 | ^ 2023-09-12T10:59:00,078 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:00,079 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:00,079 | ^~~~~~~~ 2023-09-12T10:59:00,080 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:00,080 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:00,081 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:00,082 | ^ 2023-09-12T10:59:00,082 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:00,083 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:00,083 | ^~~~~~~~ 2023-09-12T10:59:00,099 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:00,099 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:00,100 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:00,101 | ^ 2023-09-12T10:59:00,101 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:00,102 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:00,103 | ^~~~~~~~ 2023-09-12T10:59:00,105 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:00,106 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:00,107 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:00,107 | ^ 2023-09-12T10:59:00,108 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:00,109 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:00,110 | ^~~~~~~~ 2023-09-12T10:59:00,279 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:00,279 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:00,280 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:00,281 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:00,282 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:00,282 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:00,283 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:00,284 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:00,284 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:00,285 from include/openbabel/mol.h:35: 2023-09-12T10:59:00,285 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:00,286 131 | struct binary_function 2023-09-12T10:59:00,286 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:00,507 ./src/formats/abinitformat.cpp: In member function ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:59:00,507 ./src/formats/abinitformat.cpp:91:12: warning: variable ‘acell’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:59:00,508 91 | double acell[3]; // scale of lattice vectors 2023-09-12T10:59:00,508 | ^~~~~ 2023-09-12T10:59:02,889 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:59:02,890 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:59:02,890 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:02,891 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:59:02,891 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:03,224 ./src/formats/abinitformat.cpp: In member function ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:59:03,225 ./src/formats/abinitformat.cpp:218:25: warning: ‘natom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:03,225 218 | for (int j = 0; j < natom; ++j) { 2023-09-12T10:59:03,226 | ~~^~~~~~~ 2023-09-12T10:59:03,227 ./src/formats/abinitformat.cpp:82:9: note: ‘natom’ was declared here 2023-09-12T10:59:03,227 82 | int natom; 2023-09-12T10:59:03,228 | ^~~~~ 2023-09-12T10:59:03,237 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:03,237 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:03,238 inlined from ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/abinitformat.cpp:129:27: 2023-09-12T10:59:03,239 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:03,240 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:03,240 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:03,241 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:03,242 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:03,242 inlined from ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/abinitformat.cpp:138:36: 2023-09-12T10:59:03,243 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:03,244 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:03,245 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:03,847 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/abinitformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:03,847 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/abinitformat.o /tmp/cch18f2d.s 2023-09-12T10:59:03,852 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:04,079 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:04,080 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:04,080 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/abinitformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/abinitformat.' 2023-09-12T10:59:04,082 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/acesformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/acesformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:04,086 Using built-in specs. 2023-09-12T10:59:04,087 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:04,088 Target: arm-linux-gnueabihf 2023-09-12T10:59:04,088 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:04,089 Thread model: posix 2023-09-12T10:59:04,089 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:04,090 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:04,090 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/acesformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:04,091 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/acesformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase acesformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccoE8OuD.s 2023-09-12T10:59:04,099 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:04,100 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:04,101 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:04,102 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:04,102 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:04,103 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:04,104 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:04,104 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:04,105 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:04,105 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:04,106 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:04,107 #include "..." search starts here: 2023-09-12T10:59:04,107 #include <...> search starts here: 2023-09-12T10:59:04,108 /usr/include/eigen3 2023-09-12T10:59:04,109 include 2023-09-12T10:59:04,109 /usr/include/python3.11 2023-09-12T10:59:04,110 /usr/include/c++/12 2023-09-12T10:59:04,110 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:04,111 /usr/include/c++/12/backward 2023-09-12T10:59:04,111 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:04,112 /usr/local/include 2023-09-12T10:59:04,112 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:04,113 /usr/include 2023-09-12T10:59:04,113 End of search list. 2023-09-12T10:59:04,114 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:04,115 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:04,116 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:04,116 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:04,121 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:05,688 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:05,689 from include/openbabel/mol.h:43, 2023-09-12T10:59:05,690 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:05,691 from ./src/formats/acesformat.cpp:20: 2023-09-12T10:59:05,691 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:05,692 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:05,692 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:05,693 | ^ 2023-09-12T10:59:05,693 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:05,694 37 | # define UNUSED(x) x 2023-09-12T10:59:05,694 | ^ 2023-09-12T10:59:06,457 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:06,458 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:06,459 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:06,459 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:06,460 | ^ 2023-09-12T10:59:06,460 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:06,461 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:06,462 | ^~~~~~~~ 2023-09-12T10:59:06,463 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:06,463 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:06,464 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:06,465 | ^ 2023-09-12T10:59:06,466 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:06,466 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:06,467 | ^~~~~~~~ 2023-09-12T10:59:06,482 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:06,483 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:06,483 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:06,484 | ^ 2023-09-12T10:59:06,485 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:06,485 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:06,486 | ^~~~~~~~ 2023-09-12T10:59:06,488 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:06,489 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:06,490 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:06,491 | ^ 2023-09-12T10:59:06,491 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:06,492 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:06,492 | ^~~~~~~~ 2023-09-12T10:59:06,661 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:06,662 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:06,662 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:06,663 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:06,664 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:06,664 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:06,665 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:06,665 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:06,666 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:06,666 from include/openbabel/mol.h:35: 2023-09-12T10:59:06,667 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:06,668 131 | struct binary_function 2023-09-12T10:59:06,668 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:09,668 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:59:09,669 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:59:09,669 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:09,670 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:59:09,671 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:09,729 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:59:09,730 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:10,553 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:10,553 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:10,554 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:182:37: 2023-09-12T10:59:10,555 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:10,555 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:10,556 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:10,557 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:10,557 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:10,558 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:184:37: 2023-09-12T10:59:10,559 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:10,560 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:10,560 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:10,561 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:10,561 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:10,562 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:198:37: 2023-09-12T10:59:10,562 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:10,563 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:10,563 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:10,564 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:10,565 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:10,566 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:200:37: 2023-09-12T10:59:10,566 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:10,567 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:10,568 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:10,569 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:10,569 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:10,570 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:202:37: 2023-09-12T10:59:10,571 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:10,572 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:10,572 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:10,573 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:10,574 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:10,575 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:225:39: 2023-09-12T10:59:10,576 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:10,576 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:10,577 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:11,626 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/acesformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:11,627 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/acesformat.o /tmp/ccoE8OuD.s 2023-09-12T10:59:11,631 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:11,970 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:11,971 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:11,972 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/acesformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/acesformat.' 2023-09-12T10:59:11,973 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/acrformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/acrformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:11,977 Using built-in specs. 2023-09-12T10:59:11,978 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:11,978 Target: arm-linux-gnueabihf 2023-09-12T10:59:11,979 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:11,979 Thread model: posix 2023-09-12T10:59:11,980 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:11,981 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:11,981 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/acrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:11,982 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/acrformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase acrformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccWYZ3QG.s 2023-09-12T10:59:11,990 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:11,991 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:11,992 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:11,992 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:11,993 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:11,994 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:11,994 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:11,995 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:11,996 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:11,996 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:11,997 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:11,997 #include "..." search starts here: 2023-09-12T10:59:11,998 #include <...> search starts here: 2023-09-12T10:59:11,998 /usr/include/eigen3 2023-09-12T10:59:11,999 include 2023-09-12T10:59:12,000 /usr/include/python3.11 2023-09-12T10:59:12,000 /usr/include/c++/12 2023-09-12T10:59:12,001 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:12,001 /usr/include/c++/12/backward 2023-09-12T10:59:12,002 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:12,002 /usr/local/include 2023-09-12T10:59:12,003 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:12,003 /usr/include 2023-09-12T10:59:12,004 End of search list. 2023-09-12T10:59:12,005 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:12,005 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:12,007 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:12,007 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:12,008 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:14,206 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:14,207 from include/openbabel/mol.h:43, 2023-09-12T10:59:14,208 from ./src/formats/acrformat.cpp:23: 2023-09-12T10:59:14,208 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:14,209 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:14,210 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:14,210 | ^ 2023-09-12T10:59:14,211 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:14,212 37 | # define UNUSED(x) x 2023-09-12T10:59:14,217 | ^ 2023-09-12T10:59:14,978 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:14,979 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:14,980 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:14,988 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:14,993 | ^ 2023-09-12T10:59:15,013 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:15,137 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:15,245 | ^~~~~~~~ 2023-09-12T10:59:15,496 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:15,600 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:15,622 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:15,622 | ^ 2023-09-12T10:59:15,623 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:15,624 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:15,625 | ^~~~~~~~ 2023-09-12T10:59:15,626 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:15,626 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:15,627 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:15,628 | ^ 2023-09-12T10:59:15,628 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:15,629 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:15,630 | ^~~~~~~~ 2023-09-12T10:59:15,631 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:15,632 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:15,633 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:15,634 | ^ 2023-09-12T10:59:15,634 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:15,635 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:15,635 | ^~~~~~~~ 2023-09-12T10:59:15,636 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:15,637 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:15,638 from include/openbabel/obmolecformat.h:31, 2023-09-12T10:59:15,639 from ./src/formats/acrformat.cpp:24: 2023-09-12T10:59:15,639 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:15,640 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:15,641 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:15,641 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:15,642 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:15,643 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:15,644 from include/openbabel/mol.h:35: 2023-09-12T10:59:15,645 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:15,646 131 | struct binary_function 2023-09-12T10:59:15,646 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:15,774 ./src/formats/acrformat.cpp: In member function ‘virtual int OpenBabel::ACRFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T10:59:15,775 ./src/formats/acrformat.cpp:67:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T10:59:15,776 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T10:59:15,777 | ~~~~^ 2023-09-12T10:59:15,778 ./src/formats/acrformat.cpp:67:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:59:15,779 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T10:59:15,780 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:59:15,781 ./src/formats/acrformat.cpp: In member function ‘virtual bool OpenBabel::ACRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:59:15,781 ./src/formats/acrformat.cpp:113:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:59:15,782 113 | } else if (sscanf(buf, "Number of Atoms in Crystal=%d\n", &tmp)) { 2023-09-12T10:59:15,783 | ~^ ~~~~ 2023-09-12T10:59:15,783 | | | 2023-09-12T10:59:15,784 | int* unsigned int* 2023-09-12T10:59:15,785 | %d 2023-09-12T10:59:15,786 ./src/formats/acrformat.cpp:120:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:59:15,787 120 | } else if (sscanf(buf, "Number of Links in Crystal=%d\n", &tmp)) { 2023-09-12T10:59:15,788 | ~^ ~~~~ 2023-09-12T10:59:15,789 | | | 2023-09-12T10:59:15,790 | int* unsigned int* 2023-09-12T10:59:15,791 | %d 2023-09-12T10:59:17,638 ./src/formats/acrformat.cpp:137:40: warning: ‘scale’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:17,639 137 | X = atof((char*)vs[6].c_str())/scale; 2023-09-12T10:59:17,639 | ^~~~~ 2023-09-12T10:59:17,640 ./src/formats/acrformat.cpp:93:11: note: ‘scale’ was declared here 2023-09-12T10:59:17,640 93 | float scale, dtmp; 2023-09-12T10:59:17,641 | ^~~~~ 2023-09-12T10:59:17,641 ./src/formats/acrformat.cpp:159:5: warning: ‘bonds’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:17,642 159 | if ( pmol->NumBonds() != bonds ) { 2023-09-12T10:59:17,643 | ^~ 2023-09-12T10:59:17,643 ./src/formats/acrformat.cpp:92:25: note: ‘bonds’ was declared here 2023-09-12T10:59:17,644 92 | unsigned int atoms, bonds, tmp; 2023-09-12T10:59:17,644 | ^~~~~ 2023-09-12T10:59:17,645 ./src/formats/acrformat.cpp:163:12: warning: ‘atoms’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:17,645 163 | } else if ( pmol->NumAtoms() != atoms ) { 2023-09-12T10:59:17,646 | ^~ 2023-09-12T10:59:17,647 ./src/formats/acrformat.cpp:92:18: note: ‘atoms’ was declared here 2023-09-12T10:59:17,647 92 | unsigned int atoms, bonds, tmp; 2023-09-12T10:59:17,648 | ^~~~~ 2023-09-12T10:59:18,509 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/acrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:18,509 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/acrformat.o /tmp/ccWYZ3QG.s 2023-09-12T10:59:18,514 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:18,701 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:18,702 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:18,702 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/acrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/acrformat.' 2023-09-12T10:59:18,703 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/adfformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/adfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:18,707 Using built-in specs. 2023-09-12T10:59:18,708 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:18,708 Target: arm-linux-gnueabihf 2023-09-12T10:59:18,709 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:18,709 Thread model: posix 2023-09-12T10:59:18,710 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:18,710 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:18,711 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/adfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:18,711 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/adfformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase adfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cctwZvdR.s 2023-09-12T10:59:18,720 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:18,721 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:18,722 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:18,722 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:18,723 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:18,723 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:18,724 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:18,724 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:18,725 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:18,726 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:18,726 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:18,727 #include "..." search starts here: 2023-09-12T10:59:18,728 #include <...> search starts here: 2023-09-12T10:59:18,728 /usr/include/eigen3 2023-09-12T10:59:18,729 include 2023-09-12T10:59:18,730 /usr/include/python3.11 2023-09-12T10:59:18,730 /usr/include/c++/12 2023-09-12T10:59:18,731 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:18,731 /usr/include/c++/12/backward 2023-09-12T10:59:18,732 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:18,732 /usr/local/include 2023-09-12T10:59:18,732 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:18,733 /usr/include 2023-09-12T10:59:18,733 End of search list. 2023-09-12T10:59:18,734 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:18,734 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:18,735 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:18,735 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:18,742 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:20,279 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:20,279 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:20,280 from ./src/formats/adfformat.cpp:34: 2023-09-12T10:59:20,281 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:20,281 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:20,282 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:20,282 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:59:20,283 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:59:20,284 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:59:20,285 from /usr/include/c++/12/ios:42, 2023-09-12T10:59:20,285 from /usr/include/c++/12/istream:38, 2023-09-12T10:59:20,286 from /usr/include/c++/12/fstream:38, 2023-09-12T10:59:20,287 from ./src/formats/adfformat.cpp:28: 2023-09-12T10:59:20,287 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:20,288 131 | struct binary_function 2023-09-12T10:59:20,289 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:20,510 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:20,511 from include/openbabel/mol.h:43, 2023-09-12T10:59:20,511 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:20,512 from ./src/formats/adfformat.cpp:35: 2023-09-12T10:59:20,513 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:20,514 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:20,514 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:20,515 | ^ 2023-09-12T10:59:20,515 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:20,516 37 | # define UNUSED(x) x 2023-09-12T10:59:20,517 | ^ 2023-09-12T10:59:21,182 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:21,183 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:21,184 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:21,185 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:21,185 | ^ 2023-09-12T10:59:21,186 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:21,187 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:21,188 | ^~~~~~~~ 2023-09-12T10:59:21,189 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:21,190 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:21,190 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:21,191 | ^ 2023-09-12T10:59:21,191 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:21,192 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:21,192 | ^~~~~~~~ 2023-09-12T10:59:21,211 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:21,211 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:21,212 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:21,212 | ^ 2023-09-12T10:59:21,213 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:21,214 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:21,215 | ^~~~~~~~ 2023-09-12T10:59:21,218 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:21,219 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:21,220 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:21,220 | ^ 2023-09-12T10:59:21,221 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:21,222 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:21,223 | ^~~~~~~~ 2023-09-12T10:59:21,487 ./src/formats/adfformat.cpp: In member function ‘virtual bool OpenBabel::ADFInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:59:21,488 ./src/formats/adfformat.cpp:274:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2023-09-12T10:59:21,488 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2023-09-12T10:59:21,489 | ~~~~~~~~^~~ 2023-09-12T10:59:21,490 ./src/formats/adfformat.cpp:274:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:59:21,491 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2023-09-12T10:59:21,491 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:59:21,502 ./src/formats/adfformat.cpp: In member function ‘virtual int OpenBabel::OBT41Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T10:59:21,503 ./src/formats/adfformat.cpp:400:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T10:59:21,504 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2023-09-12T10:59:21,505 | ~~~~^ 2023-09-12T10:59:21,505 ./src/formats/adfformat.cpp:400:51: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:59:21,506 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2023-09-12T10:59:21,506 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:59:21,507 ./src/formats/adfformat.cpp: In member function ‘void OpenBabel::OBT41Format::AddSCFGrids(std::istream&, OpenBabel::OBGridData&)’: 2023-09-12T10:59:21,508 ./src/formats/adfformat.cpp:448:32: warning: unused parameter ‘is’ [-Wunused-parameter] 2023-09-12T10:59:21,508 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2023-09-12T10:59:21,509 | ~~~~~~~~~^~ 2023-09-12T10:59:21,510 ./src/formats/adfformat.cpp:448:48: warning: unused parameter ‘t41’ [-Wunused-parameter] 2023-09-12T10:59:21,510 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2023-09-12T10:59:21,511 | ~~~~~~~~~~~~^~~ 2023-09-12T10:59:21,513 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadBinary(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:59:21,514 ./src/formats/adfformat.cpp:533:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2023-09-12T10:59:21,514 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2023-09-12T10:59:21,515 | ~~~~~~~~^~~ 2023-09-12T10:59:21,515 ./src/formats/adfformat.cpp:533:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:59:21,516 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2023-09-12T10:59:21,517 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:59:21,522 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadASCII(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:59:21,523 ./src/formats/adfformat.cpp:590:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:59:21,524 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,525 | ^~~~~ 2023-09-12T10:59:21,525 ./src/formats/adfformat.cpp:590:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:59:21,526 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,527 | ^~~~ 2023-09-12T10:59:21,529 ./src/formats/adfformat.cpp:603:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:59:21,530 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,531 | ^~~~~ 2023-09-12T10:59:21,531 ./src/formats/adfformat.cpp:603:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:59:21,532 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,533 | ^~~~ 2023-09-12T10:59:21,549 ./src/formats/adfformat.cpp:625:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:59:21,550 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,551 | ^~~~~ 2023-09-12T10:59:21,552 ./src/formats/adfformat.cpp:625:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:59:21,553 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,553 | ^~~~ 2023-09-12T10:59:21,558 ./src/formats/adfformat.cpp:640:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:59:21,559 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,559 | ^~~~~ 2023-09-12T10:59:21,560 ./src/formats/adfformat.cpp:640:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:59:21,561 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,562 | ^~~~ 2023-09-12T10:59:21,564 ./src/formats/adfformat.cpp:655:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:59:21,564 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,565 | ^~~~~ 2023-09-12T10:59:21,566 ./src/formats/adfformat.cpp:655:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:59:21,566 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:59:21,567 | ^~~~ 2023-09-12T10:59:27,524 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:59:27,524 from ./src/formats/adfformat.cpp:30: 2023-09-12T10:59:27,525 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::OBT41Format::AtomData}; _Tp = OpenBabel::OBT41Format::AtomData; _Alloc = std::allocator]’: 2023-09-12T10:59:27,525 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:27,526 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:59:27,527 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:28,028 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::OBT41Format::AtomData}; _Tp = OpenBabel::OBT41Format::AtomData; _Alloc = std::allocator]’, 2023-09-12T10:59:28,029 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::OBT41Format::AtomData; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:28,030 inlined from ‘bool OpenBabel::OBT41Format::ReadASCII(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/adfformat.cpp:616:26: 2023-09-12T10:59:28,031 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:28,031 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:28,032 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:30,155 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/adfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:30,155 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/adfformat.o /tmp/cctwZvdR.s 2023-09-12T10:59:30,160 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:30,811 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:30,812 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:30,812 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/adfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/adfformat.' 2023-09-12T10:59:30,815 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/alchemyformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/alchemyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:30,819 Using built-in specs. 2023-09-12T10:59:30,820 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:30,820 Target: arm-linux-gnueabihf 2023-09-12T10:59:30,821 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:30,822 Thread model: posix 2023-09-12T10:59:30,822 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:30,823 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:30,823 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/alchemyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:30,824 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/alchemyformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase alchemyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cci6jCOm.s 2023-09-12T10:59:30,833 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:30,834 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:30,835 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:30,836 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:30,836 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:30,837 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:30,837 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:30,838 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:30,838 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:30,838 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:30,839 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:30,839 #include "..." search starts here: 2023-09-12T10:59:30,840 #include <...> search starts here: 2023-09-12T10:59:30,840 /usr/include/eigen3 2023-09-12T10:59:30,841 include 2023-09-12T10:59:30,841 /usr/include/python3.11 2023-09-12T10:59:30,842 /usr/include/c++/12 2023-09-12T10:59:30,842 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:30,843 /usr/include/c++/12/backward 2023-09-12T10:59:30,843 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:30,844 /usr/local/include 2023-09-12T10:59:30,844 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:30,845 /usr/include 2023-09-12T10:59:30,845 End of search list. 2023-09-12T10:59:30,845 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:30,846 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:30,847 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:30,848 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:30,859 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:32,920 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:32,921 from include/openbabel/mol.h:43, 2023-09-12T10:59:32,922 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:32,922 from ./src/formats/alchemyformat.cpp:17: 2023-09-12T10:59:32,923 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:32,923 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:32,924 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:32,925 | ^ 2023-09-12T10:59:32,925 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:32,926 37 | # define UNUSED(x) x 2023-09-12T10:59:32,927 | ^ 2023-09-12T10:59:33,695 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:33,695 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,696 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,697 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:33,698 | ^ 2023-09-12T10:59:33,698 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:33,699 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:33,699 | ^~~~~~~~ 2023-09-12T10:59:33,703 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,703 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,704 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:33,704 | ^ 2023-09-12T10:59:33,705 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:33,706 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:33,706 | ^~~~~~~~ 2023-09-12T10:59:33,724 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,725 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,725 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:33,726 | ^ 2023-09-12T10:59:33,727 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:33,727 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:33,728 | ^~~~~~~~ 2023-09-12T10:59:33,733 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,734 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,734 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:33,735 | ^ 2023-09-12T10:59:33,736 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:33,736 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:33,737 | ^~~~~~~~ 2023-09-12T10:59:33,907 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:33,908 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:33,909 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:33,909 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:33,910 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:33,911 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:33,911 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:33,912 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:33,913 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:33,913 from include/openbabel/mol.h:35: 2023-09-12T10:59:33,914 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:33,914 131 | struct binary_function 2023-09-12T10:59:33,915 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:36,801 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/alchemyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:36,801 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/alchemyformat.o /tmp/cci6jCOm.s 2023-09-12T10:59:36,806 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:36,979 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:36,980 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:36,981 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/alchemyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/alchemyformat.' 2023-09-12T10:59:36,981 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/amberformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/amberformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:36,986 Using built-in specs. 2023-09-12T10:59:36,986 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:36,987 Target: arm-linux-gnueabihf 2023-09-12T10:59:36,988 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:36,988 Thread model: posix 2023-09-12T10:59:36,989 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:36,989 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:36,990 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/amberformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:36,990 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/amberformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase amberformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccn3P4NC.s 2023-09-12T10:59:36,999 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:36,999 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:37,000 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:37,001 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:37,002 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:37,002 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:37,003 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:37,003 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:37,004 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:37,005 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:37,005 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:37,006 #include "..." search starts here: 2023-09-12T10:59:37,007 #include <...> search starts here: 2023-09-12T10:59:37,007 /usr/include/eigen3 2023-09-12T10:59:37,008 include 2023-09-12T10:59:37,008 /usr/include/python3.11 2023-09-12T10:59:37,009 /usr/include/c++/12 2023-09-12T10:59:37,009 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:37,010 /usr/include/c++/12/backward 2023-09-12T10:59:37,010 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:37,011 /usr/local/include 2023-09-12T10:59:37,011 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:37,012 /usr/include 2023-09-12T10:59:37,013 End of search list. 2023-09-12T10:59:37,013 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:37,014 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:37,015 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:37,015 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:37,019 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:38,604 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:38,605 from include/openbabel/mol.h:43, 2023-09-12T10:59:38,606 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:38,606 from ./src/formats/amberformat.cpp:17: 2023-09-12T10:59:38,607 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:38,607 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:38,608 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:38,608 | ^ 2023-09-12T10:59:38,609 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:38,609 37 | # define UNUSED(x) x 2023-09-12T10:59:38,610 | ^ 2023-09-12T10:59:39,373 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:39,374 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:39,374 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:39,375 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:39,375 | ^ 2023-09-12T10:59:39,376 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:39,376 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:39,377 | ^~~~~~~~ 2023-09-12T10:59:39,379 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:39,379 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:39,380 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:39,381 | ^ 2023-09-12T10:59:39,381 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:39,382 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:39,383 | ^~~~~~~~ 2023-09-12T10:59:39,398 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:39,399 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:39,399 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:39,400 | ^ 2023-09-12T10:59:39,401 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:39,402 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:39,402 | ^~~~~~~~ 2023-09-12T10:59:39,405 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:39,406 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:39,406 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:39,407 | ^ 2023-09-12T10:59:39,408 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:39,408 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:39,409 | ^~~~~~~~ 2023-09-12T10:59:39,579 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:39,579 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:39,580 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:39,581 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:39,581 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:39,582 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:39,583 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:39,583 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:39,584 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:39,584 from include/openbabel/mol.h:35: 2023-09-12T10:59:39,585 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:39,586 131 | struct binary_function 2023-09-12T10:59:39,586 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:42,301 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/amberformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:42,302 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/amberformat.o /tmp/ccn3P4NC.s 2023-09-12T10:59:42,306 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:42,465 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:42,466 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:42,466 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/amberformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/amberformat.' 2023-09-12T10:59:42,467 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/aoforceformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/aoforceformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:42,471 Using built-in specs. 2023-09-12T10:59:42,472 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:42,473 Target: arm-linux-gnueabihf 2023-09-12T10:59:42,473 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:42,473 Thread model: posix 2023-09-12T10:59:42,474 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:42,474 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:42,475 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/aoforceformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:42,475 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/aoforceformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase aoforceformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccSUaxWc.s 2023-09-12T10:59:42,485 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:42,485 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:42,486 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:42,487 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:42,487 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:42,488 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:42,489 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:42,489 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:42,490 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:42,491 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:42,491 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:42,492 #include "..." search starts here: 2023-09-12T10:59:42,493 #include <...> search starts here: 2023-09-12T10:59:42,493 /usr/include/eigen3 2023-09-12T10:59:42,493 include 2023-09-12T10:59:42,494 /usr/include/python3.11 2023-09-12T10:59:42,494 /usr/include/c++/12 2023-09-12T10:59:42,495 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:42,495 /usr/include/c++/12/backward 2023-09-12T10:59:42,496 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:42,496 /usr/local/include 2023-09-12T10:59:42,496 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:42,497 /usr/include 2023-09-12T10:59:42,497 End of search list. 2023-09-12T10:59:42,498 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:42,498 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:42,499 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:42,500 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:42,504 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:44,080 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:44,080 from include/openbabel/mol.h:43, 2023-09-12T10:59:44,081 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:44,081 from ./src/formats/aoforceformat.cpp:17: 2023-09-12T10:59:44,082 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:44,082 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:44,083 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:44,084 | ^ 2023-09-12T10:59:44,084 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:44,085 37 | # define UNUSED(x) x 2023-09-12T10:59:44,085 | ^ 2023-09-12T10:59:44,852 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:44,852 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,853 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,854 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:44,854 | ^ 2023-09-12T10:59:44,855 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:44,856 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:44,856 | ^~~~~~~~ 2023-09-12T10:59:44,860 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,860 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,861 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:44,862 | ^ 2023-09-12T10:59:44,862 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:44,863 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:44,863 | ^~~~~~~~ 2023-09-12T10:59:44,881 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,882 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,883 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:44,883 | ^ 2023-09-12T10:59:44,884 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:44,884 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:44,885 | ^~~~~~~~ 2023-09-12T10:59:44,890 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,890 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,891 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:44,891 | ^ 2023-09-12T10:59:44,892 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:44,892 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:44,893 | ^~~~~~~~ 2023-09-12T10:59:45,064 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:45,065 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:45,066 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:45,066 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:45,067 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:45,068 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:45,068 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:45,069 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:45,070 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:45,070 from include/openbabel/mol.h:35: 2023-09-12T10:59:45,071 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:45,072 131 | struct binary_function 2023-09-12T10:59:45,072 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:48,157 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:59:48,158 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:59:48,158 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:48,159 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:59:48,160 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:48,222 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T10:59:48,222 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:48,551 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:48,552 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:48,553 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:82:30: 2023-09-12T10:59:48,553 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:48,554 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:48,554 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:48,555 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:48,556 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:48,556 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:94:30: 2023-09-12T10:59:48,557 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:48,557 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:48,558 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:48,559 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:48,559 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:48,560 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:108:23: 2023-09-12T10:59:48,561 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:48,561 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:48,562 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:48,562 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:48,563 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:48,564 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:115:23: 2023-09-12T10:59:48,564 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:48,565 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:48,566 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:48,566 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:48,567 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:48,568 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:122:23: 2023-09-12T10:59:48,569 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:48,569 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:48,570 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:48,570 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:48,571 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T10:59:48,571 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:134:28: 2023-09-12T10:59:48,572 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T10:59:48,573 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:48,573 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:49,581 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/aoforceformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:49,581 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/aoforceformat.o /tmp/ccSUaxWc.s 2023-09-12T10:59:49,588 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:49,900 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:49,900 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:49,901 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/aoforceformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/aoforceformat.' 2023-09-12T10:59:49,902 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/asciiformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/asciiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:49,907 Using built-in specs. 2023-09-12T10:59:49,908 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:49,909 Target: arm-linux-gnueabihf 2023-09-12T10:59:49,909 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:49,910 Thread model: posix 2023-09-12T10:59:49,910 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:49,911 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:49,911 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/asciiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:49,912 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/asciiformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase asciiformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc737voT.s 2023-09-12T10:59:49,922 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:49,923 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:49,924 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:49,924 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:49,925 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:49,925 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:49,926 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:49,927 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:49,927 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:49,928 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:49,928 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:49,929 #include "..." search starts here: 2023-09-12T10:59:49,930 #include <...> search starts here: 2023-09-12T10:59:49,930 /usr/include/eigen3 2023-09-12T10:59:49,930 include 2023-09-12T10:59:49,931 /usr/include/python3.11 2023-09-12T10:59:49,931 /usr/include/c++/12 2023-09-12T10:59:49,932 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:49,932 /usr/include/c++/12/backward 2023-09-12T10:59:49,932 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:49,933 /usr/local/include 2023-09-12T10:59:49,933 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:49,934 /usr/include 2023-09-12T10:59:49,934 End of search list. 2023-09-12T10:59:49,935 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:49,935 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:49,936 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:49,936 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:49,943 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:51,523 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:51,523 from include/openbabel/mol.h:43, 2023-09-12T10:59:51,524 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:51,524 from ./src/formats/asciiformat.cpp:19: 2023-09-12T10:59:51,525 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:51,526 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:51,526 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:51,527 | ^ 2023-09-12T10:59:51,528 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:51,529 37 | # define UNUSED(x) x 2023-09-12T10:59:51,529 | ^ 2023-09-12T10:59:52,292 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:52,292 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:52,293 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:52,294 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:52,295 | ^ 2023-09-12T10:59:52,295 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:52,296 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:52,297 | ^~~~~~~~ 2023-09-12T10:59:52,298 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:52,298 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:52,299 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:52,300 | ^ 2023-09-12T10:59:52,300 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:52,301 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:52,302 | ^~~~~~~~ 2023-09-12T10:59:52,316 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:52,317 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:52,317 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:52,318 | ^ 2023-09-12T10:59:52,319 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:52,319 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:52,320 | ^~~~~~~~ 2023-09-12T10:59:52,322 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:52,323 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:52,324 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:52,324 | ^ 2023-09-12T10:59:52,325 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:52,325 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:52,326 | ^~~~~~~~ 2023-09-12T10:59:52,496 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:52,496 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:52,497 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:52,498 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:52,498 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:52,499 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:52,500 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:52,500 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:52,501 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:52,502 from include/openbabel/mol.h:35: 2023-09-12T10:59:52,502 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:52,503 131 | struct binary_function 2023-09-12T10:59:52,504 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:52,730 In file included from ./src/formats/asciiformat.cpp:22: 2023-09-12T10:59:52,731 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2023-09-12T10:59:52,731 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T10:59:52,732 34 | void SetFontFamily(const std::string &fontFamily) {} 2023-09-12T10:59:52,733 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:59:55,305 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/asciiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:55,306 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/asciiformat.o /tmp/cc737voT.s 2023-09-12T10:59:55,310 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:55,494 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T10:59:55,495 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T10:59:55,496 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/asciiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/asciiformat.' 2023-09-12T10:59:55,497 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/balstformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/balstformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:55,501 Using built-in specs. 2023-09-12T10:59:55,501 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:55,502 Target: arm-linux-gnueabihf 2023-09-12T10:59:55,502 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T10:59:55,503 Thread model: posix 2023-09-12T10:59:55,504 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:55,504 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:55,505 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/balstformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T10:59:55,506 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/balstformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase balstformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccWGSJFO.s 2023-09-12T10:59:55,514 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:55,515 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:55,516 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:55,516 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:55,517 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:55,517 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:55,517 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:55,518 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:55,518 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:55,519 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:55,519 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:55,520 #include "..." search starts here: 2023-09-12T10:59:55,521 #include <...> search starts here: 2023-09-12T10:59:55,521 /usr/include/eigen3 2023-09-12T10:59:55,522 include 2023-09-12T10:59:55,522 /usr/include/python3.11 2023-09-12T10:59:55,523 /usr/include/c++/12 2023-09-12T10:59:55,524 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:55,524 /usr/include/c++/12/backward 2023-09-12T10:59:55,525 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:55,525 /usr/local/include 2023-09-12T10:59:55,526 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:55,527 /usr/include 2023-09-12T10:59:55,527 End of search list. 2023-09-12T10:59:55,528 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:55,528 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:55,530 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:55,530 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:55,532 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:57,097 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:57,098 from include/openbabel/mol.h:43, 2023-09-12T10:59:57,098 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:57,099 from ./src/formats/balstformat.cpp:17: 2023-09-12T10:59:57,100 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:57,100 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:57,101 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:57,101 | ^ 2023-09-12T10:59:57,102 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:57,103 37 | # define UNUSED(x) x 2023-09-12T10:59:57,104 | ^ 2023-09-12T10:59:57,867 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:57,867 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:57,868 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:57,868 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:57,869 | ^ 2023-09-12T10:59:57,869 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:57,870 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:57,871 | ^~~~~~~~ 2023-09-12T10:59:57,872 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:57,872 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:57,873 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:57,874 | ^ 2023-09-12T10:59:57,874 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:57,875 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:57,876 | ^~~~~~~~ 2023-09-12T10:59:57,891 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:57,892 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:57,892 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:57,893 | ^ 2023-09-12T10:59:57,894 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:57,895 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:57,895 | ^~~~~~~~ 2023-09-12T10:59:57,897 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:57,898 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:57,899 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:57,899 | ^ 2023-09-12T10:59:57,900 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:57,901 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:57,901 | ^~~~~~~~ 2023-09-12T10:59:58,070 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:58,071 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:58,072 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:58,073 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:58,073 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:58,074 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:58,075 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:58,075 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:58,076 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:58,076 from include/openbabel/mol.h:35: 2023-09-12T10:59:58,077 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:58,077 131 | struct binary_function 2023-09-12T10:59:58,078 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:00,828 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/balstformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:00,828 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/balstformat.o /tmp/ccWGSJFO.s 2023-09-12T11:00:00,833 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:00,993 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:00,993 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:00,994 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/balstformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/balstformat.' 2023-09-12T11:00:00,994 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/bgfformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/bgfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:00,998 Using built-in specs. 2023-09-12T11:00:00,999 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:01,000 Target: arm-linux-gnueabihf 2023-09-12T11:00:01,000 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:01,001 Thread model: posix 2023-09-12T11:00:01,002 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:01,002 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:01,003 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/bgfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:01,003 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/bgfformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase bgfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccpw1qNW.s 2023-09-12T11:00:01,012 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:01,012 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:01,014 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:01,014 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:01,015 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:01,015 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:01,016 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:01,017 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:01,017 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:01,018 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:01,018 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:01,019 #include "..." search starts here: 2023-09-12T11:00:01,019 #include <...> search starts here: 2023-09-12T11:00:01,020 /usr/include/eigen3 2023-09-12T11:00:01,020 include 2023-09-12T11:00:01,021 /usr/include/python3.11 2023-09-12T11:00:01,022 /usr/include/c++/12 2023-09-12T11:00:01,022 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:01,023 /usr/include/c++/12/backward 2023-09-12T11:00:01,023 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:01,024 /usr/local/include 2023-09-12T11:00:01,025 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:01,025 /usr/include 2023-09-12T11:00:01,026 End of search list. 2023-09-12T11:00:01,026 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:01,027 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:01,028 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:01,029 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:01,032 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:02,622 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:02,622 from include/openbabel/mol.h:43, 2023-09-12T11:00:02,623 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:02,623 from ./src/formats/bgfformat.cpp:17: 2023-09-12T11:00:02,624 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:02,624 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:02,625 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:02,625 | ^ 2023-09-12T11:00:02,626 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:02,626 37 | # define UNUSED(x) x 2023-09-12T11:00:02,627 | ^ 2023-09-12T11:00:04,225 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:04,226 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:04,227 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:04,227 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:04,228 | ^ 2023-09-12T11:00:04,228 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:04,229 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:04,230 | ^~~~~~~~ 2023-09-12T11:00:04,231 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:04,232 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:04,233 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:04,233 | ^ 2023-09-12T11:00:04,234 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:04,235 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:04,235 | ^~~~~~~~ 2023-09-12T11:00:04,251 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:04,252 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:04,253 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:04,254 | ^ 2023-09-12T11:00:04,254 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:04,255 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:04,256 | ^~~~~~~~ 2023-09-12T11:00:04,258 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:04,259 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:04,260 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:04,260 | ^ 2023-09-12T11:00:04,261 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:04,262 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:04,262 | ^~~~~~~~ 2023-09-12T11:00:04,453 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:04,454 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:04,455 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:04,455 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:04,456 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:04,457 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:04,457 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:04,459 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:04,468 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:04,521 from include/openbabel/mol.h:35: 2023-09-12T11:00:04,650 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:04,854 131 | struct binary_function 2023-09-12T11:00:04,949 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:08,424 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/bgfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:08,424 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/bgfformat.o /tmp/ccpw1qNW.s 2023-09-12T11:00:08,428 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:08,663 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:08,664 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:08,665 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/bgfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/bgfformat.' 2023-09-12T11:00:08,666 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/boxformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/boxformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:08,670 Using built-in specs. 2023-09-12T11:00:08,671 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:08,671 Target: arm-linux-gnueabihf 2023-09-12T11:00:08,672 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:08,672 Thread model: posix 2023-09-12T11:00:08,673 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:08,673 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:08,674 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/boxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:08,674 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/boxformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase boxformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccohGJgo.s 2023-09-12T11:00:08,683 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:08,683 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:08,685 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:08,685 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:08,686 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:08,686 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:08,687 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:08,688 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:08,688 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:08,689 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:08,690 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:08,690 #include "..." search starts here: 2023-09-12T11:00:08,690 #include <...> search starts here: 2023-09-12T11:00:08,691 /usr/include/eigen3 2023-09-12T11:00:08,691 include 2023-09-12T11:00:08,692 /usr/include/python3.11 2023-09-12T11:00:08,692 /usr/include/c++/12 2023-09-12T11:00:08,692 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:08,693 /usr/include/c++/12/backward 2023-09-12T11:00:08,693 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:08,694 /usr/local/include 2023-09-12T11:00:08,694 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:08,695 /usr/include 2023-09-12T11:00:08,695 End of search list. 2023-09-12T11:00:08,696 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:08,696 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:08,697 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:08,697 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:08,701 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:10,270 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:10,270 from include/openbabel/mol.h:43, 2023-09-12T11:00:10,271 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:10,272 from ./src/formats/boxformat.cpp:17: 2023-09-12T11:00:10,272 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:10,273 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:10,274 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:10,274 | ^ 2023-09-12T11:00:10,275 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:10,276 37 | # define UNUSED(x) x 2023-09-12T11:00:10,276 | ^ 2023-09-12T11:00:11,041 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:11,041 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:11,042 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:11,043 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:11,044 | ^ 2023-09-12T11:00:11,044 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:11,045 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:11,046 | ^~~~~~~~ 2023-09-12T11:00:11,047 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:11,047 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:11,048 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:11,049 | ^ 2023-09-12T11:00:11,050 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:11,051 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:11,051 | ^~~~~~~~ 2023-09-12T11:00:11,065 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:11,066 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:11,066 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:11,067 | ^ 2023-09-12T11:00:11,068 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:11,068 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:11,069 | ^~~~~~~~ 2023-09-12T11:00:11,071 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:11,072 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:11,073 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:11,073 | ^ 2023-09-12T11:00:11,074 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:11,075 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:11,076 | ^~~~~~~~ 2023-09-12T11:00:11,244 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:11,245 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:11,245 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:11,246 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:11,247 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:11,248 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:11,248 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:11,249 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:11,250 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:11,250 from include/openbabel/mol.h:35: 2023-09-12T11:00:11,251 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:11,252 131 | struct binary_function 2023-09-12T11:00:11,252 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:14,268 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/boxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:14,269 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/boxformat.o /tmp/ccohGJgo.s 2023-09-12T11:00:14,273 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:14,465 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:14,465 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:14,466 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/boxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/boxformat.' 2023-09-12T11:00:14,466 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/cacaoformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/cacaoformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:14,471 Using built-in specs. 2023-09-12T11:00:14,471 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:14,472 Target: arm-linux-gnueabihf 2023-09-12T11:00:14,473 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:14,473 Thread model: posix 2023-09-12T11:00:14,474 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:14,474 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:14,475 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacaoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:14,475 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cacaoformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase cacaoformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccHQo3q7.s 2023-09-12T11:00:14,484 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:14,486 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:14,486 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:14,487 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:14,487 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:14,488 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:14,488 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:14,488 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:14,489 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:14,489 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:14,490 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:14,490 #include "..." search starts here: 2023-09-12T11:00:14,491 #include <...> search starts here: 2023-09-12T11:00:14,491 /usr/include/eigen3 2023-09-12T11:00:14,492 include 2023-09-12T11:00:14,492 /usr/include/python3.11 2023-09-12T11:00:14,493 /usr/include/c++/12 2023-09-12T11:00:14,493 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:14,495 /usr/include/c++/12/backward 2023-09-12T11:00:14,496 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:14,497 /usr/local/include 2023-09-12T11:00:14,498 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:14,498 /usr/include 2023-09-12T11:00:14,499 End of search list. 2023-09-12T11:00:14,500 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:14,501 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:14,503 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:14,503 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:14,505 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:16,068 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:16,069 from include/openbabel/mol.h:43, 2023-09-12T11:00:16,069 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:16,070 from ./src/formats/cacaoformat.cpp:17: 2023-09-12T11:00:16,071 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:16,071 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:16,072 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:16,073 | ^ 2023-09-12T11:00:16,073 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:16,074 37 | # define UNUSED(x) x 2023-09-12T11:00:16,075 | ^ 2023-09-12T11:00:16,837 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:16,838 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:16,838 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:16,839 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:16,840 | ^ 2023-09-12T11:00:16,841 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:16,841 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:16,842 | ^~~~~~~~ 2023-09-12T11:00:16,843 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:16,843 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:16,844 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:16,844 | ^ 2023-09-12T11:00:16,845 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:16,845 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:16,846 | ^~~~~~~~ 2023-09-12T11:00:16,861 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:16,862 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:16,862 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:16,863 | ^ 2023-09-12T11:00:16,864 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:16,865 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:16,866 | ^~~~~~~~ 2023-09-12T11:00:16,868 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:16,868 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:16,869 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:16,870 | ^ 2023-09-12T11:00:16,871 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:16,871 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:16,872 | ^~~~~~~~ 2023-09-12T11:00:17,041 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:17,042 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:17,043 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:17,044 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:17,044 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:17,045 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:17,046 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:17,047 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:17,047 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:17,048 from include/openbabel/mol.h:35: 2023-09-12T11:00:17,048 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:17,049 131 | struct binary_function 2023-09-12T11:00:17,049 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:20,359 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacaoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:20,360 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/cacaoformat.o /tmp/ccHQo3q7.s 2023-09-12T11:00:20,364 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:20,577 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:20,578 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:20,579 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacaoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacaoformat.' 2023-09-12T11:00:20,580 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/cacheformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/cacheformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:20,584 Using built-in specs. 2023-09-12T11:00:20,585 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:20,585 Target: arm-linux-gnueabihf 2023-09-12T11:00:20,586 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:20,587 Thread model: posix 2023-09-12T11:00:20,588 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:20,588 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:20,589 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacheformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:20,590 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cacheformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase cacheformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccsV6fCY.s 2023-09-12T11:00:20,597 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:20,598 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:20,599 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:20,599 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:20,600 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:20,600 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:20,601 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:20,602 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:20,602 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:20,603 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:20,604 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:20,604 #include "..." search starts here: 2023-09-12T11:00:20,605 #include <...> search starts here: 2023-09-12T11:00:20,605 /usr/include/eigen3 2023-09-12T11:00:20,606 include 2023-09-12T11:00:20,606 /usr/include/python3.11 2023-09-12T11:00:20,607 /usr/include/c++/12 2023-09-12T11:00:20,607 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:20,608 /usr/include/c++/12/backward 2023-09-12T11:00:20,609 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:20,609 /usr/local/include 2023-09-12T11:00:20,610 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:20,610 /usr/include 2023-09-12T11:00:20,611 End of search list. 2023-09-12T11:00:20,611 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:20,612 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:20,613 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:20,614 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:20,615 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:22,218 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:22,218 from include/openbabel/mol.h:43, 2023-09-12T11:00:22,219 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:22,220 from ./src/formats/cacheformat.cpp:16: 2023-09-12T11:00:22,220 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:22,221 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:22,221 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:22,222 | ^ 2023-09-12T11:00:22,222 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:22,223 37 | # define UNUSED(x) x 2023-09-12T11:00:22,223 | ^ 2023-09-12T11:00:22,987 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:22,988 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:22,989 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:22,990 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:22,991 | ^ 2023-09-12T11:00:22,992 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:22,992 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:22,993 | ^~~~~~~~ 2023-09-12T11:00:22,994 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:22,995 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:22,996 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:22,996 | ^ 2023-09-12T11:00:22,997 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:22,998 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:22,999 | ^~~~~~~~ 2023-09-12T11:00:23,012 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:23,012 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:23,013 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:23,014 | ^ 2023-09-12T11:00:23,014 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:23,015 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:23,016 | ^~~~~~~~ 2023-09-12T11:00:23,018 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:23,019 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:23,020 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:23,021 | ^ 2023-09-12T11:00:23,021 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:23,022 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:23,022 | ^~~~~~~~ 2023-09-12T11:00:23,191 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:23,191 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:23,192 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:23,193 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:23,193 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:23,194 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:23,194 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:23,195 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:23,195 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:23,196 from include/openbabel/mol.h:35: 2023-09-12T11:00:23,197 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:23,197 131 | struct binary_function 2023-09-12T11:00:23,198 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:25,676 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacheformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:25,677 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/cacheformat.o /tmp/ccsV6fCY.s 2023-09-12T11:00:25,681 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:25,823 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:25,824 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:25,824 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacheformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/cacheformat.' 2023-09-12T11:00:25,826 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/carformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/carformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:25,829 Using built-in specs. 2023-09-12T11:00:25,830 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:25,831 Target: arm-linux-gnueabihf 2023-09-12T11:00:25,831 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:25,832 Thread model: posix 2023-09-12T11:00:25,832 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:25,833 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:25,834 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/carformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:25,834 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/carformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase carformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccRsxFOP.s 2023-09-12T11:00:25,842 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:25,843 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:25,844 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:25,845 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:25,845 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:25,846 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:25,846 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:25,847 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:25,848 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:25,848 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:25,849 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:25,850 #include "..." search starts here: 2023-09-12T11:00:25,851 #include <...> search starts here: 2023-09-12T11:00:25,851 /usr/include/eigen3 2023-09-12T11:00:25,851 include 2023-09-12T11:00:25,852 /usr/include/python3.11 2023-09-12T11:00:25,853 /usr/include/c++/12 2023-09-12T11:00:25,853 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:25,854 /usr/include/c++/12/backward 2023-09-12T11:00:25,854 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:25,855 /usr/local/include 2023-09-12T11:00:25,855 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:25,855 /usr/include 2023-09-12T11:00:25,856 End of search list. 2023-09-12T11:00:25,856 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:25,857 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:25,858 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:25,858 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:25,860 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:27,421 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:27,422 from include/openbabel/mol.h:43, 2023-09-12T11:00:27,423 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:27,423 from ./src/formats/carformat.cpp:18: 2023-09-12T11:00:27,424 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:27,424 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:27,425 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:27,426 | ^ 2023-09-12T11:00:27,426 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:27,427 37 | # define UNUSED(x) x 2023-09-12T11:00:27,428 | ^ 2023-09-12T11:00:28,189 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:28,190 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:28,191 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:28,191 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:28,192 | ^ 2023-09-12T11:00:28,193 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:28,194 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:28,194 | ^~~~~~~~ 2023-09-12T11:00:28,195 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:28,196 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:28,196 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:28,197 | ^ 2023-09-12T11:00:28,198 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:28,199 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:28,199 | ^~~~~~~~ 2023-09-12T11:00:28,214 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:28,214 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:28,215 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:28,216 | ^ 2023-09-12T11:00:28,216 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:28,217 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:28,217 | ^~~~~~~~ 2023-09-12T11:00:28,220 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:28,221 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:28,222 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:28,222 | ^ 2023-09-12T11:00:28,223 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:28,223 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:28,224 | ^~~~~~~~ 2023-09-12T11:00:28,394 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:28,394 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:28,395 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:28,396 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:28,397 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:28,397 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:28,398 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:28,399 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:28,400 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:28,400 from include/openbabel/mol.h:35: 2023-09-12T11:00:28,401 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:28,401 131 | struct binary_function 2023-09-12T11:00:28,402 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:31,323 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/carformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:31,324 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/carformat.o /tmp/ccRsxFOP.s 2023-09-12T11:00:31,328 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:31,514 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:31,515 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:31,515 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/carformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/carformat.' 2023-09-12T11:00:31,516 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/castepformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/castepformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:31,520 Using built-in specs. 2023-09-12T11:00:31,521 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:31,521 Target: arm-linux-gnueabihf 2023-09-12T11:00:31,522 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:31,523 Thread model: posix 2023-09-12T11:00:31,523 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:31,524 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:31,524 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/castepformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:31,525 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/castepformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase castepformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccb3gLMM.s 2023-09-12T11:00:31,533 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:31,534 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:31,535 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:31,535 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:31,536 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:31,536 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:31,537 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:31,537 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:31,538 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:31,538 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:31,539 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:31,539 #include "..." search starts here: 2023-09-12T11:00:31,539 #include <...> search starts here: 2023-09-12T11:00:31,540 /usr/include/eigen3 2023-09-12T11:00:31,540 include 2023-09-12T11:00:31,541 /usr/include/python3.11 2023-09-12T11:00:31,541 /usr/include/c++/12 2023-09-12T11:00:31,542 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:31,542 /usr/include/c++/12/backward 2023-09-12T11:00:31,543 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:31,543 /usr/local/include 2023-09-12T11:00:31,544 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:31,545 /usr/include 2023-09-12T11:00:31,545 End of search list. 2023-09-12T11:00:31,546 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:31,546 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:31,548 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:31,548 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:31,551 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:33,145 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:33,146 from include/openbabel/mol.h:43, 2023-09-12T11:00:33,146 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:33,147 from ./src/formats/castepformat.cpp:16: 2023-09-12T11:00:33,148 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:33,149 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:33,149 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:33,150 | ^ 2023-09-12T11:00:33,151 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:33,151 37 | # define UNUSED(x) x 2023-09-12T11:00:33,152 | ^ 2023-09-12T11:00:33,915 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:33,916 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:33,916 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:33,917 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:33,918 | ^ 2023-09-12T11:00:33,919 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:33,920 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:33,920 | ^~~~~~~~ 2023-09-12T11:00:33,921 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:33,921 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:33,922 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:33,922 | ^ 2023-09-12T11:00:33,923 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:33,924 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:33,924 | ^~~~~~~~ 2023-09-12T11:00:33,939 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:33,940 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:33,941 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:33,941 | ^ 2023-09-12T11:00:33,942 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:33,943 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:33,943 | ^~~~~~~~ 2023-09-12T11:00:33,946 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:33,947 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:33,947 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:33,948 | ^ 2023-09-12T11:00:33,949 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:33,950 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:33,950 | ^~~~~~~~ 2023-09-12T11:00:34,119 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:34,119 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:34,120 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:34,121 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:34,122 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:34,122 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:34,123 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:34,124 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:34,125 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:34,126 from include/openbabel/mol.h:35: 2023-09-12T11:00:34,126 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:34,127 131 | struct binary_function 2023-09-12T11:00:34,127 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:34,318 ./src/formats/castepformat.cpp: In member function ‘virtual int OpenBabel::CASTEPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:00:34,319 ./src/formats/castepformat.cpp:50:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:00:34,320 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:00:34,320 | ~~~~^ 2023-09-12T11:00:34,321 ./src/formats/castepformat.cpp:50:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:00:34,321 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:00:34,322 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:00:36,791 ./src/formats/castepformat.cpp: In member function ‘virtual bool OpenBabel::CASTEPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:36,791 ./src/formats/castepformat.cpp:203:17: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:00:36,792 203 | snprintf(tag, BUFF_SIZE, "%f", enthalpy); 2023-09-12T11:00:36,793 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:36,793 ./src/formats/castepformat.cpp:86:30: note: ‘enthalpy’ was declared here 2023-09-12T11:00:36,794 86 | double pressure, volume, enthalpy; 2023-09-12T11:00:36,795 | ^~~~~~~~ 2023-09-12T11:00:36,796 ./src/formats/castepformat.cpp:187:21: warning: ‘volume’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:00:36,796 187 | pv = volume * pressure * GPA_A3_TO_KCAL_PER_MOL; 2023-09-12T11:00:36,797 | ~~~~~~~^~~~~~~~~~ 2023-09-12T11:00:36,798 ./src/formats/castepformat.cpp:86:22: note: ‘volume’ was declared here 2023-09-12T11:00:36,798 86 | double pressure, volume, enthalpy; 2023-09-12T11:00:36,799 | ^~~~~~ 2023-09-12T11:00:36,800 ./src/formats/castepformat.cpp:187:21: warning: ‘pressure’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:00:36,800 187 | pv = volume * pressure * GPA_A3_TO_KCAL_PER_MOL; 2023-09-12T11:00:36,801 | ~~~~~~~^~~~~~~~~~ 2023-09-12T11:00:36,802 ./src/formats/castepformat.cpp:86:12: note: ‘pressure’ was declared here 2023-09-12T11:00:36,802 86 | double pressure, volume, enthalpy; 2023-09-12T11:00:36,803 | ^~~~~~~~ 2023-09-12T11:00:37,412 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/castepformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:37,413 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/castepformat.o /tmp/ccb3gLMM.s 2023-09-12T11:00:37,417 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:37,631 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:37,632 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:37,633 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/castepformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/castepformat.' 2023-09-12T11:00:37,633 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/cccformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/cccformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:37,637 Using built-in specs. 2023-09-12T11:00:37,638 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:37,639 Target: arm-linux-gnueabihf 2023-09-12T11:00:37,639 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:37,640 Thread model: posix 2023-09-12T11:00:37,640 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:37,641 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:37,642 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cccformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:37,642 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cccformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase cccformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccDBWEWg.s 2023-09-12T11:00:37,651 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:37,651 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:37,653 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:37,653 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:37,654 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:37,654 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:37,654 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:37,655 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:37,655 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:37,656 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:37,656 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:37,657 #include "..." search starts here: 2023-09-12T11:00:37,657 #include <...> search starts here: 2023-09-12T11:00:37,657 /usr/include/eigen3 2023-09-12T11:00:37,658 include 2023-09-12T11:00:37,658 /usr/include/python3.11 2023-09-12T11:00:37,658 /usr/include/c++/12 2023-09-12T11:00:37,659 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:37,659 /usr/include/c++/12/backward 2023-09-12T11:00:37,660 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:37,660 /usr/local/include 2023-09-12T11:00:37,661 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:37,661 /usr/include 2023-09-12T11:00:37,662 End of search list. 2023-09-12T11:00:37,662 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:37,663 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:37,665 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:37,665 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:37,669 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:39,229 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:39,230 from include/openbabel/mol.h:43, 2023-09-12T11:00:39,231 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:39,231 from ./src/formats/cccformat.cpp:17: 2023-09-12T11:00:39,232 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:39,232 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:39,233 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:39,234 | ^ 2023-09-12T11:00:39,235 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:39,235 37 | # define UNUSED(x) x 2023-09-12T11:00:39,236 | ^ 2023-09-12T11:00:39,999 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:40,000 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:40,001 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:40,001 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:40,002 | ^ 2023-09-12T11:00:40,003 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:40,004 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:40,005 | ^~~~~~~~ 2023-09-12T11:00:40,005 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:40,006 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:40,006 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:40,007 | ^ 2023-09-12T11:00:40,008 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:40,008 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:40,009 | ^~~~~~~~ 2023-09-12T11:00:40,024 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:40,024 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:40,025 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:40,025 | ^ 2023-09-12T11:00:40,026 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:40,027 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:40,027 | ^~~~~~~~ 2023-09-12T11:00:40,030 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:40,031 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:40,032 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:40,032 | ^ 2023-09-12T11:00:40,033 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:40,034 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:40,035 | ^~~~~~~~ 2023-09-12T11:00:40,203 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:40,204 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:40,205 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:40,205 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:40,206 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:40,207 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:40,207 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:40,208 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:40,209 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:40,210 from include/openbabel/mol.h:35: 2023-09-12T11:00:40,210 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:40,211 131 | struct binary_function 2023-09-12T11:00:40,212 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:42,782 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cccformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:42,783 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/cccformat.o /tmp/ccDBWEWg.s 2023-09-12T11:00:42,788 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:42,933 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:42,933 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:42,934 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cccformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/cccformat.' 2023-09-12T11:00:42,934 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/chem3dformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/chem3dformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:42,939 Using built-in specs. 2023-09-12T11:00:42,939 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:42,940 Target: arm-linux-gnueabihf 2023-09-12T11:00:42,941 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:42,941 Thread model: posix 2023-09-12T11:00:42,942 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:42,942 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:42,943 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chem3dformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:42,944 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chem3dformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase chem3dformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccS6jjKu.s 2023-09-12T11:00:42,952 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:42,953 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:42,953 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:42,954 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:42,954 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:42,955 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:42,955 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:42,956 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:42,957 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:42,957 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:42,958 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:42,958 #include "..." search starts here: 2023-09-12T11:00:42,959 #include <...> search starts here: 2023-09-12T11:00:42,960 /usr/include/eigen3 2023-09-12T11:00:42,960 include 2023-09-12T11:00:42,961 /usr/include/python3.11 2023-09-12T11:00:42,961 /usr/include/c++/12 2023-09-12T11:00:42,962 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:42,963 /usr/include/c++/12/backward 2023-09-12T11:00:42,963 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:42,964 /usr/local/include 2023-09-12T11:00:42,965 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:42,965 /usr/include 2023-09-12T11:00:42,966 End of search list. 2023-09-12T11:00:42,966 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:42,967 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:42,968 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:42,968 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:42,970 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:44,625 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:44,626 from include/openbabel/mol.h:43, 2023-09-12T11:00:44,627 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:44,627 from ./src/formats/chem3dformat.cpp:18: 2023-09-12T11:00:44,628 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:44,629 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:44,629 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:44,630 | ^ 2023-09-12T11:00:44,631 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:44,631 37 | # define UNUSED(x) x 2023-09-12T11:00:44,632 | ^ 2023-09-12T11:00:45,297 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:45,298 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:45,298 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:45,299 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:45,299 | ^ 2023-09-12T11:00:45,300 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:45,300 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:45,301 | ^~~~~~~~ 2023-09-12T11:00:45,302 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:45,303 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:45,303 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:45,304 | ^ 2023-09-12T11:00:45,305 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:45,306 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:45,306 | ^~~~~~~~ 2023-09-12T11:00:45,321 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:45,322 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:45,322 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:45,323 | ^ 2023-09-12T11:00:45,324 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:45,324 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:45,325 | ^~~~~~~~ 2023-09-12T11:00:45,328 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:45,328 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:45,329 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:45,330 | ^ 2023-09-12T11:00:45,330 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:45,331 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:45,332 | ^~~~~~~~ 2023-09-12T11:00:45,501 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:45,502 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:45,502 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:45,503 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:45,503 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:45,504 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:45,504 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:45,505 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:00:45,505 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:00:45,506 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:00:45,506 from /usr/include/c++/12/ios:42, 2023-09-12T11:00:45,507 from /usr/include/c++/12/ostream:38, 2023-09-12T11:00:45,507 from include/openbabel/math/matrix3x3.h:24, 2023-09-12T11:00:45,508 from ./src/formats/chem3dformat.cpp:17: 2023-09-12T11:00:45,509 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:45,509 131 | struct binary_function 2023-09-12T11:00:45,510 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:47,887 ./src/formats/chem3dformat.cpp: In static member function ‘static bool OpenBabel::CHEM3D1Format::WriteChem3d(std::ostream&, OpenBabel::OBMol&, const char*)’: 2023-09-12T11:00:47,888 ./src/formats/chem3dformat.cpp:298:52: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 4 [-Wformat-truncation=] 2023-09-12T11:00:47,888 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2023-09-12T11:00:47,889 | ^~ 2023-09-12T11:00:47,890 ./src/formats/chem3dformat.cpp:298:51: note: directive argument in the range [-536870912, 536873461] 2023-09-12T11:00:47,891 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2023-09-12T11:00:47,891 | ^~~~ 2023-09-12T11:00:47,892 ./src/formats/chem3dformat.cpp:298:21: note: ‘snprintf’ output between 2 and 11 bytes into a destination of size 4 2023-09-12T11:00:47,893 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2023-09-12T11:00:47,894 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:48,468 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chem3dformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:48,468 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/chem3dformat.o /tmp/ccS6jjKu.s 2023-09-12T11:00:48,473 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:48,867 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:00:48,868 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:00:48,869 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chem3dformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/chem3dformat.' 2023-09-12T11:00:48,870 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/chemdrawcdx.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawcdx.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:48,873 Using built-in specs. 2023-09-12T11:00:48,874 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:48,875 Target: arm-linux-gnueabihf 2023-09-12T11:00:48,875 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:00:48,876 Thread model: posix 2023-09-12T11:00:48,876 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:48,877 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:48,877 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawcdx.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:00:48,878 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemdrawcdx.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase chemdrawcdx.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc9PogL4.s 2023-09-12T11:00:48,886 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:48,887 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:48,888 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:48,889 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:48,889 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:48,889 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:48,890 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:48,890 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:48,891 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:48,891 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:48,892 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:48,892 #include "..." search starts here: 2023-09-12T11:00:48,892 #include <...> search starts here: 2023-09-12T11:00:48,893 /usr/include/eigen3 2023-09-12T11:00:48,893 include 2023-09-12T11:00:48,894 /usr/include/python3.11 2023-09-12T11:00:48,894 /usr/include/c++/12 2023-09-12T11:00:48,895 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:48,895 /usr/include/c++/12/backward 2023-09-12T11:00:48,895 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:48,896 /usr/local/include 2023-09-12T11:00:48,896 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:48,897 /usr/include 2023-09-12T11:00:48,897 End of search list. 2023-09-12T11:00:48,898 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:48,898 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:48,900 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:48,900 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:48,904 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:50,492 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:50,492 from include/openbabel/mol.h:43, 2023-09-12T11:00:50,493 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:50,494 from ./src/formats/chemdrawcdx.cpp:17: 2023-09-12T11:00:50,495 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:50,495 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:50,496 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:50,497 | ^ 2023-09-12T11:00:50,497 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:50,498 37 | # define UNUSED(x) x 2023-09-12T11:00:50,499 | ^ 2023-09-12T11:00:51,262 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:51,263 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:51,263 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:51,264 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:51,265 | ^ 2023-09-12T11:00:51,265 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:51,266 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:51,267 | ^~~~~~~~ 2023-09-12T11:00:51,267 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:51,268 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:51,269 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:51,269 | ^ 2023-09-12T11:00:51,270 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:51,270 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:51,271 | ^~~~~~~~ 2023-09-12T11:00:51,286 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:51,287 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:51,287 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:51,288 | ^ 2023-09-12T11:00:51,289 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:51,289 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:51,290 | ^~~~~~~~ 2023-09-12T11:00:51,293 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:51,293 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:51,294 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:51,295 | ^ 2023-09-12T11:00:51,295 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:51,296 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:51,297 | ^~~~~~~~ 2023-09-12T11:00:51,466 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:51,467 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:51,468 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:51,468 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:51,469 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:51,470 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:51,471 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:51,471 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:51,472 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:51,473 from include/openbabel/mol.h:35: 2023-09-12T11:00:51,473 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:51,474 131 | struct binary_function 2023-09-12T11:00:51,475 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:52,129 ./src/formats/chemdrawcdx.cpp: In member function ‘virtual bool OpenBabel::ChemDrawBinaryXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:52,130 ./src/formats/chemdrawcdx.cpp:205:50: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2023-09-12T11:00:52,130 205 | bool ChemDrawBinaryXFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) 2023-09-12T11:00:52,131 | ~~~~~~~~^~~ 2023-09-12T11:00:52,177 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoReaction(OpenBabel::CDXReader&, OpenBabel::OBReaction*)’: 2023-09-12T11:00:52,178 ./src/formats/chemdrawcdx.cpp:331:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:00:52,178 331 | for(unsigned i=0;iNumAtoms();++idx) 2023-09-12T11:00:52,272 | ~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:52,277 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2023-09-12T11:00:52,278 ./src/formats/chemdrawcdx.cpp:454:27: warning: variable ‘hasElement’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:00:52,279 454 | bool isAlias=false, hasElement=false; 2023-09-12T11:00:52,280 | ^~~~~~~~~~ 2023-09-12T11:00:52,283 ./src/formats/chemdrawcdx.cpp:446:84: warning: unused parameter ‘updown’ [-Wunused-parameter] 2023-09-12T11:00:52,284 446 | map& atommap, map& updown) 2023-09-12T11:00:52,285 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-09-12T11:00:54,295 ./src/formats/chemdrawcdx.cpp: In member function ‘std::string OpenBabel::ChemDrawBinaryXFormat::DoText(OpenBabel::CDXReader&)’: 2023-09-12T11:00:54,296 ./src/formats/chemdrawcdx.cpp:625:13: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T11:00:54,296 625 | ss >> text; 2023-09-12T11:00:54,297 | ^~~~ 2023-09-12T11:00:54,298 ./src/formats/chemdrawcdx.cpp:626:5: note: here 2023-09-12T11:00:54,298 626 | default: 2023-09-12T11:00:54,299 | ^~~~~~~ 2023-09-12T11:01:00,829 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2023-09-12T11:01:00,830 ./src/formats/chemdrawcdx.cpp:591:28: warning: ‘endIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:01:00,831 591 | if(!order || !bgnIdx || !endIdx) 2023-09-12T11:01:00,831 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:01:00,832 ./src/formats/chemdrawcdx.cpp:550:28: note: ‘endIdx’ was declared here 2023-09-12T11:01:00,833 550 | int order=1, bgnIdx, endIdx ; 2023-09-12T11:01:00,833 | ^~~~~~ 2023-09-12T11:01:00,834 ./src/formats/chemdrawcdx.cpp:591:17: warning: ‘bgnIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:01:00,835 591 | if(!order || !bgnIdx || !endIdx) 2023-09-12T11:01:00,835 | ~~~~~~~^~~~~~~~~~ 2023-09-12T11:01:00,836 ./src/formats/chemdrawcdx.cpp:550:20: note: ‘bgnIdx’ was declared here 2023-09-12T11:01:00,836 550 | int order=1, bgnIdx, endIdx ; 2023-09-12T11:01:00,837 | ^~~~~~ 2023-09-12T11:01:02,343 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawcdx.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:02,344 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawcdx.o /tmp/cc9PogL4.s 2023-09-12T11:01:02,350 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:03,141 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:01:03,142 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:01:03,142 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawcdx.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawcdx.' 2023-09-12T11:01:03,145 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/chemdrawct.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawct.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:03,150 Using built-in specs. 2023-09-12T11:01:03,151 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:03,152 Target: arm-linux-gnueabihf 2023-09-12T11:01:03,152 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:01:03,153 Thread model: posix 2023-09-12T11:01:03,153 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:03,154 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:03,154 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawct.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:03,155 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemdrawct.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase chemdrawct.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc7oE8v4.s 2023-09-12T11:01:03,164 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:03,164 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:03,165 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:03,166 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:03,166 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:03,167 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:03,167 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:03,168 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:03,169 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:03,169 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:03,170 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:03,170 #include "..." search starts here: 2023-09-12T11:01:03,171 #include <...> search starts here: 2023-09-12T11:01:03,171 /usr/include/eigen3 2023-09-12T11:01:03,172 include 2023-09-12T11:01:03,172 /usr/include/python3.11 2023-09-12T11:01:03,173 /usr/include/c++/12 2023-09-12T11:01:03,173 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:03,174 /usr/include/c++/12/backward 2023-09-12T11:01:03,174 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:03,175 /usr/local/include 2023-09-12T11:01:03,175 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:03,176 /usr/include 2023-09-12T11:01:03,177 End of search list. 2023-09-12T11:01:03,177 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:03,178 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:03,179 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:03,180 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:03,183 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:04,751 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:04,752 from include/openbabel/mol.h:43, 2023-09-12T11:01:04,752 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:04,753 from ./src/formats/chemdrawct.cpp:16: 2023-09-12T11:01:04,753 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:04,754 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:04,754 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:04,755 | ^ 2023-09-12T11:01:04,756 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:04,756 37 | # define UNUSED(x) x 2023-09-12T11:01:04,757 | ^ 2023-09-12T11:01:05,522 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:05,522 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:05,523 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:05,523 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:05,524 | ^ 2023-09-12T11:01:05,524 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:05,525 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:05,526 | ^~~~~~~~ 2023-09-12T11:01:05,528 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:05,529 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:05,529 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:05,530 | ^ 2023-09-12T11:01:05,531 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:05,531 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:05,532 | ^~~~~~~~ 2023-09-12T11:01:05,548 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:05,549 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:05,549 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:05,550 | ^ 2023-09-12T11:01:05,551 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:05,551 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:05,552 | ^~~~~~~~ 2023-09-12T11:01:05,556 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:05,556 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:05,557 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:05,558 | ^ 2023-09-12T11:01:05,559 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:05,559 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:05,560 | ^~~~~~~~ 2023-09-12T11:01:05,730 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:05,730 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:05,731 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:05,731 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:05,732 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:05,733 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:05,733 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:05,734 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:05,734 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:05,735 from include/openbabel/mol.h:35: 2023-09-12T11:01:05,735 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:05,736 131 | struct binary_function 2023-09-12T11:01:05,737 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:05,942 ./src/formats/chemdrawct.cpp: In member function ‘virtual bool OpenBabel::ChemDrawFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:01:05,943 ./src/formats/chemdrawct.cpp:130:22: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:01:05,944 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2023-09-12T11:01:05,944 | ~^ ~~~~~~~ 2023-09-12T11:01:05,945 | | | 2023-09-12T11:01:05,946 | int* unsigned int* 2023-09-12T11:01:05,946 | %d 2023-09-12T11:01:05,947 ./src/formats/chemdrawct.cpp:130:25: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:01:05,948 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2023-09-12T11:01:05,948 | ~^ ~~~~~~~ 2023-09-12T11:01:05,949 | | | 2023-09-12T11:01:05,949 | int* unsigned int* 2023-09-12T11:01:05,950 | %d 2023-09-12T11:01:05,951 ./src/formats/chemdrawct.cpp:153:32: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:01:05,951 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2023-09-12T11:01:05,952 | ~^ ~~~~ 2023-09-12T11:01:05,953 | | | 2023-09-12T11:01:05,953 | int* unsigned int* 2023-09-12T11:01:05,954 | %d 2023-09-12T11:01:05,955 ./src/formats/chemdrawct.cpp:153:34: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:01:05,956 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2023-09-12T11:01:05,956 | ~^ ~~~~ 2023-09-12T11:01:05,957 | | | 2023-09-12T11:01:05,957 | int* unsigned int* 2023-09-12T11:01:05,958 | %d 2023-09-12T11:01:05,958 ./src/formats/chemdrawct.cpp:153:36: warning: format ‘%d’ expects argument of type ‘int*’, but argument 5 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:01:05,959 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2023-09-12T11:01:05,960 | ~^ ~~~~~~ 2023-09-12T11:01:05,960 | | | 2023-09-12T11:01:05,961 | int* unsigned int* 2023-09-12T11:01:05,961 | %d 2023-09-12T11:01:08,429 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawct.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:08,430 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawct.o /tmp/cc7oE8v4.s 2023-09-12T11:01:08,434 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:08,603 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:01:08,603 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:01:08,604 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawct.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemdrawct.' 2023-09-12T11:01:08,604 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/chemkinformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/chemkinformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:08,609 Using built-in specs. 2023-09-12T11:01:08,610 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:08,611 Target: arm-linux-gnueabihf 2023-09-12T11:01:08,611 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:01:08,612 Thread model: posix 2023-09-12T11:01:08,613 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:08,613 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:08,614 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemkinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:08,614 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemkinformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase chemkinformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cchzMNRg.s 2023-09-12T11:01:08,623 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:08,624 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:08,625 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:08,626 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:08,626 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:08,627 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:08,628 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:08,628 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:08,629 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:08,630 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:08,630 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:08,631 #include "..." search starts here: 2023-09-12T11:01:08,631 #include <...> search starts here: 2023-09-12T11:01:08,632 /usr/include/eigen3 2023-09-12T11:01:08,632 include 2023-09-12T11:01:08,633 /usr/include/python3.11 2023-09-12T11:01:08,633 /usr/include/c++/12 2023-09-12T11:01:08,634 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:08,634 /usr/include/c++/12/backward 2023-09-12T11:01:08,635 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:08,636 /usr/local/include 2023-09-12T11:01:08,636 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:08,637 /usr/include 2023-09-12T11:01:08,638 End of search list. 2023-09-12T11:01:08,638 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:08,639 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:08,641 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:08,641 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:08,648 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:10,380 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:10,380 from include/openbabel/mol.h:43, 2023-09-12T11:01:10,381 from ./src/formats/chemkinformat.cpp:25: 2023-09-12T11:01:10,381 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:10,382 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:10,382 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:10,383 | ^ 2023-09-12T11:01:10,383 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:10,384 37 | # define UNUSED(x) x 2023-09-12T11:01:10,384 | ^ 2023-09-12T11:01:11,152 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:11,153 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:11,153 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:11,154 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:11,154 | ^ 2023-09-12T11:01:11,155 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:11,156 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:11,157 | ^~~~~~~~ 2023-09-12T11:01:11,159 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:11,160 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:11,161 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:11,161 | ^ 2023-09-12T11:01:11,162 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:11,163 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:11,164 | ^~~~~~~~ 2023-09-12T11:01:11,178 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:11,179 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:11,180 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:11,181 | ^ 2023-09-12T11:01:11,182 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:11,182 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:11,183 | ^~~~~~~~ 2023-09-12T11:01:11,185 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:11,186 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:11,186 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:11,187 | ^ 2023-09-12T11:01:11,187 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:11,188 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:11,189 | ^~~~~~~~ 2023-09-12T11:01:11,358 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:11,359 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:11,360 from ./src/formats/chemkinformat.cpp:27: 2023-09-12T11:01:11,360 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:11,361 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:11,361 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:11,362 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:11,363 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:01:11,363 from ./src/formats/chemkinformat.cpp:18: 2023-09-12T11:01:11,364 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:11,364 131 | struct binary_function 2023-09-12T11:01:11,365 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:11,716 In file included from ./src/formats/chemkinformat.cpp:29: 2023-09-12T11:01:11,717 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:11,718 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T11:01:11,718 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2023-09-12T11:01:11,719 | ~~~~~~~~^~~~~~ 2023-09-12T11:01:11,738 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:11,739 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T11:01:11,740 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2023-09-12T11:01:11,740 | ~~~~~~~~^~~~~~ 2023-09-12T11:01:11,901 ./src/formats/chemkinformat.cpp: In member function ‘bool OpenBabel::ChemKinFormat::ReadReactionQualifierLines(std::istream&, OpenBabel::OBReaction*)’: 2023-09-12T11:01:11,902 ./src/formats/chemkinformat.cpp:634:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:01:11,903 634 | for(int i=0;iReactionType) 2023-09-12T11:01:12,014 | ^ 2023-09-12T11:01:12,015 ./src/formats/chemkinformat.cpp:905:11: warning: enumeration value ‘THREEBODY’ not handled in switch [-Wswitch] 2023-09-12T11:01:12,049 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘ARRHENIUS’ not handled in switch [-Wswitch] 2023-09-12T11:01:12,049 984 | switch(pRD->ReactionType) 2023-09-12T11:01:12,050 | ^ 2023-09-12T11:01:12,050 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘SRI’ not handled in switch [-Wswitch] 2023-09-12T11:01:26,361 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemkinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:26,361 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/chemkinformat.o /tmp/cchzMNRg.s 2023-09-12T11:01:26,366 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:27,592 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:01:27,593 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:01:27,594 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemkinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemkinformat.' 2023-09-12T11:01:27,598 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/chemtoolformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/chemtoolformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:27,602 Using built-in specs. 2023-09-12T11:01:27,603 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:27,603 Target: arm-linux-gnueabihf 2023-09-12T11:01:27,604 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:01:27,604 Thread model: posix 2023-09-12T11:01:27,605 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:27,605 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:27,606 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemtoolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:27,606 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemtoolformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase chemtoolformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccAAJZeZ.s 2023-09-12T11:01:27,616 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:27,617 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:27,618 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:27,619 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:27,619 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:27,620 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:27,620 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:27,621 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:27,622 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:27,622 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:27,623 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:27,624 #include "..." search starts here: 2023-09-12T11:01:27,624 #include <...> search starts here: 2023-09-12T11:01:27,625 /usr/include/eigen3 2023-09-12T11:01:27,625 include 2023-09-12T11:01:27,626 /usr/include/python3.11 2023-09-12T11:01:27,626 /usr/include/c++/12 2023-09-12T11:01:27,627 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:27,628 /usr/include/c++/12/backward 2023-09-12T11:01:27,628 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:27,629 /usr/local/include 2023-09-12T11:01:27,629 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:27,630 /usr/include 2023-09-12T11:01:27,630 End of search list. 2023-09-12T11:01:27,631 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:27,632 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:27,633 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:27,633 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:27,635 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:29,206 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:29,207 from include/openbabel/mol.h:43, 2023-09-12T11:01:29,208 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:29,208 from ./src/formats/chemtoolformat.cpp:19: 2023-09-12T11:01:29,209 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:29,209 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:29,210 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:29,210 | ^ 2023-09-12T11:01:29,211 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:29,211 37 | # define UNUSED(x) x 2023-09-12T11:01:29,212 | ^ 2023-09-12T11:01:29,980 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:29,981 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:29,981 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:29,982 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:29,982 | ^ 2023-09-12T11:01:29,983 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:29,984 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:29,985 | ^~~~~~~~ 2023-09-12T11:01:29,986 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:29,986 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:29,987 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:29,988 | ^ 2023-09-12T11:01:29,989 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:29,989 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:29,990 | ^~~~~~~~ 2023-09-12T11:01:30,005 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:30,005 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:30,006 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:30,007 | ^ 2023-09-12T11:01:30,007 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:30,008 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:30,009 | ^~~~~~~~ 2023-09-12T11:01:30,011 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:30,012 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:30,013 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:30,013 | ^ 2023-09-12T11:01:30,014 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:30,014 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:30,015 | ^~~~~~~~ 2023-09-12T11:01:30,185 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:30,186 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:30,186 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:30,187 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:30,188 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:30,188 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:30,189 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:30,190 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:30,190 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:30,191 from include/openbabel/mol.h:35: 2023-09-12T11:01:30,191 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:30,192 131 | struct binary_function 2023-09-12T11:01:30,193 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:32,737 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemtoolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:32,738 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/chemtoolformat.o /tmp/ccAAJZeZ.s 2023-09-12T11:01:32,742 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:32,888 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:01:32,889 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:01:32,890 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemtoolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/chemtoolformat.' 2023-09-12T11:01:32,891 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/cifformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/cifformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:32,894 Using built-in specs. 2023-09-12T11:01:32,895 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:32,896 Target: arm-linux-gnueabihf 2023-09-12T11:01:32,896 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:01:32,897 Thread model: posix 2023-09-12T11:01:32,897 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:32,898 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:32,898 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:32,899 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cifformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase cifformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccMX6dor.s 2023-09-12T11:01:32,908 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:32,908 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:32,909 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:32,910 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:32,911 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:32,911 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:32,912 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:32,912 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:32,913 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:32,914 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:32,915 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:32,915 #include "..." search starts here: 2023-09-12T11:01:32,915 #include <...> search starts here: 2023-09-12T11:01:32,916 /usr/include/eigen3 2023-09-12T11:01:32,916 include 2023-09-12T11:01:32,917 /usr/include/python3.11 2023-09-12T11:01:32,917 /usr/include/c++/12 2023-09-12T11:01:32,918 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:32,918 /usr/include/c++/12/backward 2023-09-12T11:01:32,918 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:32,919 /usr/local/include 2023-09-12T11:01:32,919 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:32,920 /usr/include 2023-09-12T11:01:32,920 End of search list. 2023-09-12T11:01:32,920 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:32,921 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:32,922 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:32,922 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:32,927 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:34,510 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:34,511 from include/openbabel/mol.h:43, 2023-09-12T11:01:34,512 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:34,512 from ./src/formats/cifformat.cpp:20: 2023-09-12T11:01:34,513 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:34,513 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:34,514 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:34,515 | ^ 2023-09-12T11:01:34,516 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:34,516 37 | # define UNUSED(x) x 2023-09-12T11:01:34,517 | ^ 2023-09-12T11:01:35,290 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:35,291 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:35,292 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:35,292 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:35,293 | ^ 2023-09-12T11:01:35,294 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:35,295 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:35,295 | ^~~~~~~~ 2023-09-12T11:01:35,296 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:35,297 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:35,298 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:35,298 | ^ 2023-09-12T11:01:35,299 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:35,300 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:35,301 | ^~~~~~~~ 2023-09-12T11:01:35,316 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:35,317 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:35,317 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:35,318 | ^ 2023-09-12T11:01:35,318 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:35,319 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:35,320 | ^~~~~~~~ 2023-09-12T11:01:35,323 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:35,323 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:35,324 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:35,325 | ^ 2023-09-12T11:01:35,325 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:35,326 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:35,327 | ^~~~~~~~ 2023-09-12T11:01:35,497 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:35,497 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:35,498 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:35,499 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:35,500 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:35,500 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:35,501 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:35,502 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:35,503 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:35,503 from include/openbabel/mol.h:35: 2023-09-12T11:01:35,504 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:35,504 131 | struct binary_function 2023-09-12T11:01:35,505 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:36,098 ./src/formats/cifformat.cpp: In member function ‘void OpenBabel::CIFData::CalcMatrices()’: 2023-09-12T11:01:36,099 ./src/formats/cifformat.cpp:900:11: warning: variable ‘aa’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:01:36,099 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T11:01:36,100 | ^~ 2023-09-12T11:01:36,101 ./src/formats/cifformat.cpp:900:14: warning: variable ‘bb’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:01:36,101 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T11:01:36,102 | ^~ 2023-09-12T11:01:36,103 ./src/formats/cifformat.cpp:900:27: warning: variable ‘betaa’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:01:36,104 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T11:01:36,105 | ^~~~~ 2023-09-12T11:01:36,105 ./src/formats/cifformat.cpp:900:33: warning: variable ‘gammaa’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:01:36,106 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T11:01:36,107 | ^~~~~~ 2023-09-12T11:01:48,075 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:01:48,075 from include/openbabel/mol.h:37: 2023-09-12T11:01:48,076 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:01:48,077 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:01:48,077 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:01:48,078 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:48,298 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:01:48,298 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:01:48,299 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:876:39: 2023-09-12T11:01:48,300 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:01:48,300 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:01:48,301 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:48,302 512 | std::tuple(__k), 2023-09-12T11:01:48,302 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:48,303 513 | std::tuple<>()); 2023-09-12T11:01:48,304 | ~~~~~~~~~~~~~~~ 2023-09-12T11:01:48,305 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:01:48,305 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:887:37: 2023-09-12T11:01:48,306 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:01:48,307 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:01:48,307 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:48,308 512 | std::tuple(__k), 2023-09-12T11:01:48,309 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:48,309 513 | std::tuple<>()); 2023-09-12T11:01:48,310 | ~~~~~~~~~~~~~~~ 2023-09-12T11:01:54,793 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:54,794 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/cifformat.o /tmp/ccMX6dor.s 2023-09-12T11:01:54,799 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:56,372 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:01:56,373 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:01:56,373 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/cifformat.' 2023-09-12T11:01:56,379 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/confabreport.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/confabreport.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:56,383 Using built-in specs. 2023-09-12T11:01:56,384 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:56,385 Target: arm-linux-gnueabihf 2023-09-12T11:01:56,385 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:01:56,386 Thread model: posix 2023-09-12T11:01:56,387 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:56,387 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:56,388 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/confabreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:01:56,388 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/confabreport.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase confabreport.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc8abunp.s 2023-09-12T11:01:56,397 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:56,397 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:56,398 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:56,399 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:56,399 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:56,400 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:56,400 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:56,401 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:56,401 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:56,402 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:56,403 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:56,403 #include "..." search starts here: 2023-09-12T11:01:56,404 #include <...> search starts here: 2023-09-12T11:01:56,404 /usr/include/eigen3 2023-09-12T11:01:56,405 include 2023-09-12T11:01:56,405 /usr/include/python3.11 2023-09-12T11:01:56,406 /usr/include/c++/12 2023-09-12T11:01:56,407 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:56,407 /usr/include/c++/12/backward 2023-09-12T11:01:56,408 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:56,409 /usr/local/include 2023-09-12T11:01:56,409 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:56,410 /usr/include 2023-09-12T11:01:56,411 End of search list. 2023-09-12T11:01:56,411 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:56,412 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:56,413 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:56,413 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:56,416 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:58,183 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:58,184 from include/openbabel/mol.h:43, 2023-09-12T11:01:58,184 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:58,185 from ./src/formats/confabreport.cpp:34: 2023-09-12T11:01:58,185 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:58,186 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:58,186 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:58,187 | ^ 2023-09-12T11:01:58,187 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:58,188 37 | # define UNUSED(x) x 2023-09-12T11:01:58,188 | ^ 2023-09-12T11:01:58,959 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:58,960 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:58,961 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:58,962 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:58,962 | ^ 2023-09-12T11:01:58,963 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:58,964 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:58,965 | ^~~~~~~~ 2023-09-12T11:01:58,966 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:58,967 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:58,967 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:58,968 | ^ 2023-09-12T11:01:58,969 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:58,969 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:58,970 | ^~~~~~~~ 2023-09-12T11:01:58,988 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:58,989 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:58,989 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:58,990 | ^ 2023-09-12T11:01:58,991 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:58,992 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:58,993 | ^~~~~~~~ 2023-09-12T11:01:58,996 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:58,997 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:58,998 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:58,998 | ^ 2023-09-12T11:01:58,999 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:58,999 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:59,000 | ^~~~~~~~ 2023-09-12T11:01:59,170 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:59,171 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:59,171 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:59,172 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:59,173 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:59,173 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:59,174 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:59,175 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:59,176 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:59,176 from include/openbabel/mol.h:35: 2023-09-12T11:01:59,177 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:59,178 131 | struct binary_function 2023-09-12T11:01:59,179 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:00,958 ./src/formats/confabreport.cpp: In member function ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’: 2023-09-12T11:02:00,959 ./src/formats/confabreport.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:02:00,959 128 | for (int i=1; i < binvals.size(); i++) 2023-09-12T11:02:00,960 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T11:02:00,961 ./src/formats/confabreport.cpp:133:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:02:00,962 133 | for (int i=1; i < cumbins.size(); i++) 2023-09-12T11:02:00,963 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T11:02:03,128 In file included from /usr/include/c++/12/bits/stl_algo.h:60, 2023-09-12T11:02:03,133 from /usr/include/c++/12/algorithm:61, 2023-09-12T11:02:03,201 from include/openbabel/ring.h:24, 2023-09-12T11:02:03,313 from include/openbabel/mol.h:51: 2023-09-12T11:02:03,314 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2023-09-12T11:02:03,315 /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,318 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T11:02:03,319 | ^~~~~~~~~~~~~ 2023-09-12T11:02:03,332 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2023-09-12T11:02:03,372 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,377 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T11:02:03,395 | ^~~~~~~~~~~~~~~~ 2023-09-12T11:02:03,405 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,489 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2023-09-12T11:02:03,493 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,499 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T11:02:03,712 | ^~~~~~~~~~~~~~~~ 2023-09-12T11:02:03,712 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,713 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,714 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T11:02:03,715 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:03,958 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2023-09-12T11:02:03,959 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, 2023-09-12T11:02:03,960 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2023-09-12T11:02:03,960 /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,961 1937 | std::__introsort_loop(__first, __last, 2023-09-12T11:02:03,962 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:02:03,962 1938 | std::__lg(__last - __first) * 2, 2023-09-12T11:02:03,963 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:03,964 1939 | __comp); 2023-09-12T11:02:03,964 | ~~~~~~~ 2023-09-12T11:02:03,965 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2023-09-12T11:02:03,966 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-12T11:02:03,966 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, 2023-09-12T11:02:03,967 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2023-09-12T11:02:03,968 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,968 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T11:02:03,968 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:03,969 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:03,970 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T11:02:03,970 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:04,101 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:02:04,101 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:02:04,102 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:04,102 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:04,103 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:04,217 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:04,218 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:04,218 inlined from ‘virtual bool OpenBabel::ConfabReport::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/confabreport.cpp:212:17: 2023-09-12T11:02:04,219 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:04,220 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:04,220 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:04,928 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/confabreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:04,929 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/confabreport.o /tmp/cc8abunp.s 2023-09-12T11:02:04,936 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:05,240 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:05,241 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:05,242 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/confabreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/confabreport.' 2023-09-12T11:02:05,243 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/copyformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/copyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:05,248 Using built-in specs. 2023-09-12T11:02:05,249 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:05,249 Target: arm-linux-gnueabihf 2023-09-12T11:02:05,250 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:05,250 Thread model: posix 2023-09-12T11:02:05,251 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:05,251 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:05,252 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/copyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:05,252 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/copyformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase copyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccyrsxK0.s 2023-09-12T11:02:05,262 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:05,263 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:05,264 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:05,264 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:05,265 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:05,265 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:05,266 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:05,266 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:05,267 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:05,267 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:05,268 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:05,268 #include "..." search starts here: 2023-09-12T11:02:05,268 #include <...> search starts here: 2023-09-12T11:02:05,269 /usr/include/eigen3 2023-09-12T11:02:05,269 include 2023-09-12T11:02:05,270 /usr/include/python3.11 2023-09-12T11:02:05,270 /usr/include/c++/12 2023-09-12T11:02:05,271 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:05,271 /usr/include/c++/12/backward 2023-09-12T11:02:05,272 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:05,272 /usr/local/include 2023-09-12T11:02:05,273 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:05,273 /usr/include 2023-09-12T11:02:05,274 End of search list. 2023-09-12T11:02:05,274 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:05,275 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:05,276 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:05,277 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:05,280 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:06,741 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:06,741 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:06,742 from ./src/formats/copyformat.cpp:14: 2023-09-12T11:02:06,743 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:06,744 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:06,745 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:06,745 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:02:06,746 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:02:06,746 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:02:06,747 from /usr/include/c++/12/ios:42, 2023-09-12T11:02:06,748 from /usr/include/c++/12/ostream:38, 2023-09-12T11:02:06,748 from /usr/include/c++/12/iostream:39, 2023-09-12T11:02:06,749 from include/openbabel/obconversion.h:24: 2023-09-12T11:02:06,750 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:06,750 131 | struct binary_function 2023-09-12T11:02:06,751 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:07,618 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/copyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:07,619 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/copyformat.o /tmp/ccyrsxK0.s 2023-09-12T11:02:07,623 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:07,684 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:07,685 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:07,687 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/copyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/copyformat.' 2023-09-12T11:02:07,688 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/crkformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/crkformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:07,697 Using built-in specs. 2023-09-12T11:02:07,698 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:07,699 Target: arm-linux-gnueabihf 2023-09-12T11:02:07,700 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:07,701 Thread model: posix 2023-09-12T11:02:07,703 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:07,704 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:07,705 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/crkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:07,706 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/crkformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase crkformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccKhTgtt.s 2023-09-12T11:02:07,715 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:07,716 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:07,717 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:07,718 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:07,718 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:07,718 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:07,719 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:07,719 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:07,720 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:07,720 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:07,721 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:07,722 #include "..." search starts here: 2023-09-12T11:02:07,722 #include <...> search starts here: 2023-09-12T11:02:07,723 /usr/include/eigen3 2023-09-12T11:02:07,723 include 2023-09-12T11:02:07,724 /usr/include/python3.11 2023-09-12T11:02:07,725 /usr/include/c++/12 2023-09-12T11:02:07,725 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:07,726 /usr/include/c++/12/backward 2023-09-12T11:02:07,726 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:07,727 /usr/local/include 2023-09-12T11:02:07,728 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:07,728 /usr/include 2023-09-12T11:02:07,729 End of search list. 2023-09-12T11:02:07,730 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:07,730 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:07,732 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:07,732 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:07,733 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:09,306 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:09,306 from include/openbabel/mol.h:43, 2023-09-12T11:02:09,307 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:09,308 from ./src/formats/crkformat.cpp:16: 2023-09-12T11:02:09,308 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:09,309 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:09,310 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:09,310 | ^ 2023-09-12T11:02:09,311 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:09,312 37 | # define UNUSED(x) x 2023-09-12T11:02:09,313 | ^ 2023-09-12T11:02:10,077 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:10,078 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:10,078 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:10,079 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:10,079 | ^ 2023-09-12T11:02:10,080 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:10,080 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:10,081 | ^~~~~~~~ 2023-09-12T11:02:10,082 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:10,082 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:10,083 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:10,084 | ^ 2023-09-12T11:02:10,084 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:10,085 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:10,085 | ^~~~~~~~ 2023-09-12T11:02:10,101 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:10,102 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:10,102 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:10,103 | ^ 2023-09-12T11:02:10,104 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:10,104 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:10,105 | ^~~~~~~~ 2023-09-12T11:02:10,107 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:10,108 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:10,109 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:10,109 | ^ 2023-09-12T11:02:10,110 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:10,111 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:10,111 | ^~~~~~~~ 2023-09-12T11:02:10,281 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:10,281 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:10,282 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:10,283 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:10,284 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:10,284 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:10,285 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:10,285 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:02:10,286 from /usr/include/c++/12/vector:66, 2023-09-12T11:02:10,286 from include/openbabel/mol.h:35: 2023-09-12T11:02:10,287 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:10,288 131 | struct binary_function 2023-09-12T11:02:10,288 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:13,330 ./src/formats/crkformat.cpp: In static member function ‘static bool OpenBabel::CRK2DFormat::ReadCRK(std::istream&, OpenBabel::OBMol&, const char*)’: 2023-09-12T11:02:13,330 ./src/formats/crkformat.cpp:304:38: warning: ‘bondStyle’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,331 304 | stbondStyle[numBonds]=bondStyle; 2023-09-12T11:02:13,331 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:02:13,332 ./src/formats/crkformat.cpp:243:25: note: ‘bondStyle’ was declared here 2023-09-12T11:02:13,332 243 | int bondFrom,bondTo,bondStyle; 2023-09-12T11:02:13,333 | ^~~~~~~~~ 2023-09-12T11:02:13,334 ./src/formats/crkformat.cpp:302:35: warning: ‘bondTo’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,334 302 | stbondTo[numBonds]=bondTo; 2023-09-12T11:02:13,335 | ~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:02:13,336 ./src/formats/crkformat.cpp:243:18: note: ‘bondTo’ was declared here 2023-09-12T11:02:13,336 243 | int bondFrom,bondTo,bondStyle; 2023-09-12T11:02:13,337 | ^~~~~~ 2023-09-12T11:02:13,338 ./src/formats/crkformat.cpp:301:37: warning: ‘bondFrom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,339 301 | stbondFrom[numBonds]=bondFrom; 2023-09-12T11:02:13,340 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:02:13,340 ./src/formats/crkformat.cpp:243:9: note: ‘bondFrom’ was declared here 2023-09-12T11:02:13,341 243 | int bondFrom,bondTo,bondStyle; 2023-09-12T11:02:13,342 | ^~~~~~~~ 2023-09-12T11:02:13,343 ./src/formats/crkformat.cpp:287:36: warning: ‘atomCharge’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,344 287 | atm.SetFormalCharge((int)atomCharge); 2023-09-12T11:02:13,344 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:02:13,345 ./src/formats/crkformat.cpp:242:30: note: ‘atomCharge’ was declared here 2023-09-12T11:02:13,346 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T11:02:13,346 | ^~~~~~~~~~ 2023-09-12T11:02:13,347 ./src/formats/crkformat.cpp:286:30: warning: ‘atomZ’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,348 286 | atm.SetVector(atomX,atomY,atomZ); 2023-09-12T11:02:13,348 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:13,349 ./src/formats/crkformat.cpp:242:24: note: ‘atomZ’ was declared here 2023-09-12T11:02:13,350 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T11:02:13,351 | ^~~~~ 2023-09-12T11:02:13,351 ./src/formats/crkformat.cpp:286:30: warning: ‘atomY’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,352 286 | atm.SetVector(atomX,atomY,atomZ); 2023-09-12T11:02:13,353 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:13,354 ./src/formats/crkformat.cpp:242:18: note: ‘atomY’ was declared here 2023-09-12T11:02:13,355 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T11:02:13,355 | ^~~~~ 2023-09-12T11:02:13,356 ./src/formats/crkformat.cpp:286:30: warning: ‘atomX’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,357 286 | atm.SetVector(atomX,atomY,atomZ); 2023-09-12T11:02:13,357 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:13,358 ./src/formats/crkformat.cpp:242:12: note: ‘atomX’ was declared here 2023-09-12T11:02:13,358 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T11:02:13,359 | ^~~~~ 2023-09-12T11:02:13,359 In member function ‘void OpenBabel::OBAtom::SetAtomicNum(int)’, 2023-09-12T11:02:13,360 inlined from ‘static bool OpenBabel::CRK2DFormat::ReadCRK(std::istream&, OpenBabel::OBMol&, const char*)’ at ./src/formats/crkformat.cpp:285:33: 2023-09-12T11:02:13,361 include/openbabel/atom.h:144:52: warning: ‘atomNumber’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,361 144 | void SetAtomicNum(int atomicnum) { _ele = (char)atomicnum; } 2023-09-12T11:02:13,362 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:13,362 ./src/formats/crkformat.cpp: In static member function ‘static bool OpenBabel::CRK2DFormat::ReadCRK(std::istream&, OpenBabel::OBMol&, const char*)’: 2023-09-12T11:02:13,363 ./src/formats/crkformat.cpp:241:16: note: ‘atomNumber’ was declared here 2023-09-12T11:02:13,363 241 | int atomID,atomNumber; 2023-09-12T11:02:13,364 | ^~~~~~~~~~ 2023-09-12T11:02:13,365 ./src/formats/crkformat.cpp:283:37: warning: ‘atomID’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:13,365 283 | statomID[numAtoms++]=atomID; 2023-09-12T11:02:13,366 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:02:13,367 ./src/formats/crkformat.cpp:241:9: note: ‘atomID’ was declared here 2023-09-12T11:02:13,368 241 | int atomID,atomNumber; 2023-09-12T11:02:13,369 | ^~~~~~ 2023-09-12T11:02:14,214 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/crkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:14,215 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/crkformat.o /tmp/ccKhTgtt.s 2023-09-12T11:02:14,219 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:14,486 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:14,487 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:14,487 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/crkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/crkformat.' 2023-09-12T11:02:14,489 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/crystal09format.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/crystal09format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:14,493 Using built-in specs. 2023-09-12T11:02:14,494 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:14,494 Target: arm-linux-gnueabihf 2023-09-12T11:02:14,495 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:14,495 Thread model: posix 2023-09-12T11:02:14,496 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:14,496 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:14,497 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/crystal09format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:14,498 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/crystal09format.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase crystal09format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccVzAXyu.s 2023-09-12T11:02:14,506 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:14,507 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:14,508 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:14,509 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:14,509 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:14,510 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:14,510 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:14,511 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:14,512 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:14,513 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:14,513 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:14,513 #include "..." search starts here: 2023-09-12T11:02:14,514 #include <...> search starts here: 2023-09-12T11:02:14,514 /usr/include/eigen3 2023-09-12T11:02:14,515 include 2023-09-12T11:02:14,515 /usr/include/python3.11 2023-09-12T11:02:14,516 /usr/include/c++/12 2023-09-12T11:02:14,516 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:14,516 /usr/include/c++/12/backward 2023-09-12T11:02:14,517 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:14,517 /usr/local/include 2023-09-12T11:02:14,518 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:14,518 /usr/include 2023-09-12T11:02:14,519 End of search list. 2023-09-12T11:02:14,519 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:14,520 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:14,521 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:14,521 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:14,524 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:16,207 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:16,208 from include/openbabel/mol.h:43, 2023-09-12T11:02:16,209 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:16,209 from ./src/formats/crystal09format.cpp:21: 2023-09-12T11:02:16,210 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:16,210 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:16,211 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:16,212 | ^ 2023-09-12T11:02:16,213 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:16,213 37 | # define UNUSED(x) x 2023-09-12T11:02:16,214 | ^ 2023-09-12T11:02:16,910 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:16,911 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:16,911 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:16,912 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:16,913 | ^ 2023-09-12T11:02:16,913 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:16,914 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:16,915 | ^~~~~~~~ 2023-09-12T11:02:16,915 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:16,916 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:16,917 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:16,918 | ^ 2023-09-12T11:02:16,918 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:16,919 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:16,920 | ^~~~~~~~ 2023-09-12T11:02:16,934 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:16,935 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:16,935 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:16,936 | ^ 2023-09-12T11:02:16,937 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:16,937 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:16,938 | ^~~~~~~~ 2023-09-12T11:02:16,941 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:16,941 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:16,942 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:16,942 | ^ 2023-09-12T11:02:16,943 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:16,944 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:16,945 | ^~~~~~~~ 2023-09-12T11:02:17,114 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:17,115 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:17,116 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:17,116 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:17,117 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:17,118 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:17,119 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:17,119 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:02:17,120 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:02:17,121 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:02:17,121 from /usr/include/c++/12/ios:42, 2023-09-12T11:02:17,122 from /usr/include/c++/12/istream:38, 2023-09-12T11:02:17,123 from /usr/include/c++/12/fstream:38, 2023-09-12T11:02:17,123 from ./src/formats/crystal09format.cpp:15: 2023-09-12T11:02:17,124 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:17,125 131 | struct binary_function 2023-09-12T11:02:17,125 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:20,228 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:02:20,228 from ./src/formats/crystal09format.cpp:18: 2023-09-12T11:02:20,229 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:02:20,230 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:20,231 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:20,231 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:20,278 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:02:20,279 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:20,339 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:02:20,340 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:22,138 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:02:22,139 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:22,139 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:219:25: 2023-09-12T11:02:22,140 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,140 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:22,141 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:22,142 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:22,143 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:220:30: 2023-09-12T11:02:22,143 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,144 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:22,145 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:22,146 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:22,146 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,147 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:246:27: 2023-09-12T11:02:22,148 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,148 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,149 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,150 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:22,150 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,151 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:252:27: 2023-09-12T11:02:22,152 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,153 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,153 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,154 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:22,154 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,155 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:258:27: 2023-09-12T11:02:22,155 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,156 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,157 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,157 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:22,158 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,158 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:261:24: 2023-09-12T11:02:22,159 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,159 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,160 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,161 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:22,162 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,163 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:262:24: 2023-09-12T11:02:22,163 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,164 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,165 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,166 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:22,167 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,167 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:263:26: 2023-09-12T11:02:22,169 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,169 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,170 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,170 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:22,171 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,171 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:264:25: 2023-09-12T11:02:22,172 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,173 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,174 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,174 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:22,175 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,176 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:265:25: 2023-09-12T11:02:22,177 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,177 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,178 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,179 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:22,180 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:22,180 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:266:24: 2023-09-12T11:02:22,181 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:22,182 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:22,182 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:23,662 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/crystal09format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:23,662 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/crystal09format.o /tmp/ccVzAXyu.s 2023-09-12T11:02:23,667 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:24,063 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:24,063 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:24,064 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/crystal09format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/crystal09format.' 2023-09-12T11:02:24,066 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/cssrformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/cssrformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:24,070 Using built-in specs. 2023-09-12T11:02:24,071 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:24,071 Target: arm-linux-gnueabihf 2023-09-12T11:02:24,072 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:24,072 Thread model: posix 2023-09-12T11:02:24,073 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:24,073 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:24,074 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cssrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:24,075 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cssrformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase cssrformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccE5CQa5.s 2023-09-12T11:02:24,083 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:24,084 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:24,085 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:24,085 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:24,086 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:24,086 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:24,087 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:24,087 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:24,088 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:24,088 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:24,089 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:24,089 #include "..." search starts here: 2023-09-12T11:02:24,090 #include <...> search starts here: 2023-09-12T11:02:24,090 /usr/include/eigen3 2023-09-12T11:02:24,091 include 2023-09-12T11:02:24,091 /usr/include/python3.11 2023-09-12T11:02:24,092 /usr/include/c++/12 2023-09-12T11:02:24,092 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:24,093 /usr/include/c++/12/backward 2023-09-12T11:02:24,094 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:24,094 /usr/local/include 2023-09-12T11:02:24,095 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:24,096 /usr/include 2023-09-12T11:02:24,096 End of search list. 2023-09-12T11:02:24,097 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:24,098 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:24,099 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:24,099 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:24,102 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:25,676 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:25,677 from include/openbabel/mol.h:43, 2023-09-12T11:02:25,677 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:25,678 from ./src/formats/cssrformat.cpp:17: 2023-09-12T11:02:25,679 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:25,679 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:25,680 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:25,681 | ^ 2023-09-12T11:02:25,681 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:25,682 37 | # define UNUSED(x) x 2023-09-12T11:02:25,683 | ^ 2023-09-12T11:02:26,449 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:26,449 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:26,450 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:26,450 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:26,451 | ^ 2023-09-12T11:02:26,451 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:26,452 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:26,452 | ^~~~~~~~ 2023-09-12T11:02:26,454 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:26,455 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:26,456 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:26,456 | ^ 2023-09-12T11:02:26,457 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:26,458 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:26,458 | ^~~~~~~~ 2023-09-12T11:02:26,475 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:26,475 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:26,476 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:26,477 | ^ 2023-09-12T11:02:26,478 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:26,478 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:26,479 | ^~~~~~~~ 2023-09-12T11:02:26,482 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:26,483 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:26,483 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:26,484 | ^ 2023-09-12T11:02:26,485 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:26,486 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:26,486 | ^~~~~~~~ 2023-09-12T11:02:26,658 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:26,658 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:26,659 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:26,659 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:26,660 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:26,660 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:26,661 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:26,661 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:02:26,662 from /usr/include/c++/12/vector:66, 2023-09-12T11:02:26,662 from include/openbabel/mol.h:35: 2023-09-12T11:02:26,663 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:26,663 131 | struct binary_function 2023-09-12T11:02:26,664 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:29,256 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cssrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:29,257 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/cssrformat.o /tmp/ccE5CQa5.s 2023-09-12T11:02:29,262 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:29,426 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:29,427 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:29,427 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/cssrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/cssrformat.' 2023-09-12T11:02:29,428 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/daltonformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/daltonformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:29,432 Using built-in specs. 2023-09-12T11:02:29,433 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:29,434 Target: arm-linux-gnueabihf 2023-09-12T11:02:29,434 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:29,435 Thread model: posix 2023-09-12T11:02:29,436 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:29,436 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:29,437 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/daltonformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:29,437 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/daltonformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase daltonformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccx5tJWA.s 2023-09-12T11:02:29,446 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:29,446 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:29,448 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:29,448 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:29,449 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:29,449 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:29,450 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:29,451 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:29,451 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:29,452 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:29,452 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:29,453 #include "..." search starts here: 2023-09-12T11:02:29,453 #include <...> search starts here: 2023-09-12T11:02:29,454 /usr/include/eigen3 2023-09-12T11:02:29,454 include 2023-09-12T11:02:29,455 /usr/include/python3.11 2023-09-12T11:02:29,456 /usr/include/c++/12 2023-09-12T11:02:29,456 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:29,457 /usr/include/c++/12/backward 2023-09-12T11:02:29,458 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:29,458 /usr/local/include 2023-09-12T11:02:29,459 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:29,460 /usr/include 2023-09-12T11:02:29,460 End of search list. 2023-09-12T11:02:29,461 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:29,462 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:29,463 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:29,463 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:29,466 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:31,041 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:31,042 from include/openbabel/mol.h:43, 2023-09-12T11:02:31,042 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:31,043 from ./src/formats/daltonformat.cpp:15: 2023-09-12T11:02:31,043 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:31,044 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:31,045 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:31,045 | ^ 2023-09-12T11:02:31,046 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:31,046 37 | # define UNUSED(x) x 2023-09-12T11:02:31,047 | ^ 2023-09-12T11:02:31,808 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:31,812 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:31,813 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:31,814 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:31,816 | ^ 2023-09-12T11:02:31,820 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:31,821 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:31,822 | ^~~~~~~~ 2023-09-12T11:02:31,823 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:31,824 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:31,825 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:31,825 | ^ 2023-09-12T11:02:31,826 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:31,827 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:31,827 | ^~~~~~~~ 2023-09-12T11:02:31,833 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:31,836 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:31,837 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:31,840 | ^ 2023-09-12T11:02:31,841 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:31,842 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:31,843 | ^~~~~~~~ 2023-09-12T11:02:31,844 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:31,848 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:31,849 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:31,850 | ^ 2023-09-12T11:02:31,851 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:31,851 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:31,852 | ^~~~~~~~ 2023-09-12T11:02:32,012 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:32,013 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:32,014 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:32,014 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:32,015 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:32,016 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:32,016 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:32,017 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:02:32,018 from /usr/include/c++/12/vector:66, 2023-09-12T11:02:32,019 from include/openbabel/mol.h:35: 2023-09-12T11:02:32,019 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:32,020 131 | struct binary_function 2023-09-12T11:02:32,021 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:32,226 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:32,227 ./src/formats/daltonformat.cpp:142:9: warning: variable ‘atomcount’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:02:32,228 142 | int atomcount = 0; // for each atom type 2023-09-12T11:02:32,229 | ^~~~~~~~~ 2023-09-12T11:02:32,234 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:32,235 ./src/formats/daltonformat.cpp:306:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:02:32,236 306 | if(atom->GetAtomicNum() != atomtype) 2023-09-12T11:02:32,237 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T11:02:32,239 ./src/formats/daltonformat.cpp:326:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:02:32,239 326 | if(atom->GetAtomicNum() != atomtype) 2023-09-12T11:02:32,240 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T11:02:35,781 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/daltonformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:35,782 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/daltonformat.o /tmp/ccx5tJWA.s 2023-09-12T11:02:35,787 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:36,032 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:36,032 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:36,033 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/daltonformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/daltonformat.' 2023-09-12T11:02:36,035 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/dlpolyformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/dlpolyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:36,038 Using built-in specs. 2023-09-12T11:02:36,039 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:36,040 Target: arm-linux-gnueabihf 2023-09-12T11:02:36,041 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:36,041 Thread model: posix 2023-09-12T11:02:36,042 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:36,042 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:36,043 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/dlpolyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:36,044 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/dlpolyformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase dlpolyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccSgdvkC.s 2023-09-12T11:02:36,053 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:36,054 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:36,055 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:36,055 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:36,055 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:36,056 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:36,056 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:36,057 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:36,057 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:36,058 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:36,058 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:36,059 #include "..." search starts here: 2023-09-12T11:02:36,059 #include <...> search starts here: 2023-09-12T11:02:36,060 /usr/include/eigen3 2023-09-12T11:02:36,061 include 2023-09-12T11:02:36,061 /usr/include/python3.11 2023-09-12T11:02:36,062 /usr/include/c++/12 2023-09-12T11:02:36,063 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:36,063 /usr/include/c++/12/backward 2023-09-12T11:02:36,064 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:36,065 /usr/local/include 2023-09-12T11:02:36,065 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:36,066 /usr/include 2023-09-12T11:02:36,066 End of search list. 2023-09-12T11:02:36,067 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:36,068 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:36,069 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:36,070 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:36,079 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:37,660 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:37,661 from include/openbabel/mol.h:43, 2023-09-12T11:02:37,661 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:37,662 from ./src/formats/dlpolyformat.cpp:14: 2023-09-12T11:02:37,663 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:37,663 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:37,664 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:37,664 | ^ 2023-09-12T11:02:37,665 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:37,666 37 | # define UNUSED(x) x 2023-09-12T11:02:37,667 | ^ 2023-09-12T11:02:38,433 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:38,434 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:38,434 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:38,435 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:38,435 | ^ 2023-09-12T11:02:38,436 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:38,436 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:38,437 | ^~~~~~~~ 2023-09-12T11:02:38,441 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:38,441 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:38,442 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:38,442 | ^ 2023-09-12T11:02:38,443 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:38,443 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:38,444 | ^~~~~~~~ 2023-09-12T11:02:38,462 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:38,462 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:38,463 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:38,464 | ^ 2023-09-12T11:02:38,465 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:38,465 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:38,466 | ^~~~~~~~ 2023-09-12T11:02:38,471 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:38,471 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:38,472 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:38,472 | ^ 2023-09-12T11:02:38,473 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:38,474 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:38,474 | ^~~~~~~~ 2023-09-12T11:02:38,648 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:38,648 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:38,649 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:38,650 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:38,651 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:38,651 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:38,652 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:38,652 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:02:38,652 from /usr/include/c++/12/vector:66, 2023-09-12T11:02:38,653 from include/openbabel/mol.h:35: 2023-09-12T11:02:38,653 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:38,654 131 | struct binary_function 2023-09-12T11:02:38,654 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:39,084 ./src/formats/dlpolyformat.cpp: In member function ‘bool OpenBabel::DlpolyInputReader::ParseUnitCell(std::istream&, OpenBabel::OBMol&)’: 2023-09-12T11:02:39,085 ./src/formats/dlpolyformat.cpp:147:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:02:39,085 147 | bool ok; 2023-09-12T11:02:39,085 | ^~ 2023-09-12T11:02:44,901 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:02:44,902 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:02:44,902 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:44,903 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:44,904 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:45,232 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:45,233 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:02:45,233 inlined from ‘bool OpenBabel::DlpolyInputReader::ReadAtom(std::istream&, OpenBabel::OBMol&)’ at ./src/formats/dlpolyformat.cpp:242:25: 2023-09-12T11:02:45,234 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:02:45,234 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:45,235 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:47,775 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/dlpolyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:47,776 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/dlpolyformat.o /tmp/ccSgdvkC.s 2023-09-12T11:02:47,781 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:48,558 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:48,558 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:48,559 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/dlpolyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/dlpolyformat.' 2023-09-12T11:02:48,563 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/dmolformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/dmolformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:48,567 Using built-in specs. 2023-09-12T11:02:48,567 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:48,568 Target: arm-linux-gnueabihf 2023-09-12T11:02:48,568 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:48,569 Thread model: posix 2023-09-12T11:02:48,569 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:48,570 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:48,570 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/dmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:48,571 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/dmolformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase dmolformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccDT4dUW.s 2023-09-12T11:02:48,580 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:48,581 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:48,582 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:48,583 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:48,583 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:48,583 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:48,584 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:48,584 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:48,585 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:48,585 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:48,586 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:48,586 #include "..." search starts here: 2023-09-12T11:02:48,587 #include <...> search starts here: 2023-09-12T11:02:48,587 /usr/include/eigen3 2023-09-12T11:02:48,588 include 2023-09-12T11:02:48,588 /usr/include/python3.11 2023-09-12T11:02:48,588 /usr/include/c++/12 2023-09-12T11:02:48,589 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:48,589 /usr/include/c++/12/backward 2023-09-12T11:02:48,590 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:48,590 /usr/local/include 2023-09-12T11:02:48,591 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:48,591 /usr/include 2023-09-12T11:02:48,592 End of search list. 2023-09-12T11:02:48,593 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:48,593 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:48,594 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:48,595 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:48,598 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:50,171 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:50,171 from include/openbabel/mol.h:43, 2023-09-12T11:02:50,172 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:50,173 from ./src/formats/dmolformat.cpp:16: 2023-09-12T11:02:50,174 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:50,174 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:50,175 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:50,176 | ^ 2023-09-12T11:02:50,177 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:50,177 37 | # define UNUSED(x) x 2023-09-12T11:02:50,178 | ^ 2023-09-12T11:02:50,940 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:50,941 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:50,942 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:50,943 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:50,943 | ^ 2023-09-12T11:02:50,944 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:50,945 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:50,946 | ^~~~~~~~ 2023-09-12T11:02:50,946 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:50,947 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:50,948 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:50,948 | ^ 2023-09-12T11:02:50,949 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:50,949 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:50,950 | ^~~~~~~~ 2023-09-12T11:02:50,965 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:50,965 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:50,966 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:50,966 | ^ 2023-09-12T11:02:50,967 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:50,968 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:50,968 | ^~~~~~~~ 2023-09-12T11:02:50,971 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:50,972 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:50,972 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:50,973 | ^ 2023-09-12T11:02:50,974 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:50,975 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:50,976 | ^~~~~~~~ 2023-09-12T11:02:51,144 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:51,145 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:51,145 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:51,146 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:51,147 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:51,147 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:51,148 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:51,149 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:02:51,149 from /usr/include/c++/12/vector:66, 2023-09-12T11:02:51,150 from include/openbabel/mol.h:35: 2023-09-12T11:02:51,151 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:51,152 131 | struct binary_function 2023-09-12T11:02:51,152 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:54,197 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/dmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:54,197 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/dmolformat.o /tmp/ccDT4dUW.s 2023-09-12T11:02:54,202 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:54,400 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:54,400 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:54,401 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/dmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/dmolformat.' 2023-09-12T11:02:54,402 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/exampleformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/exampleformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:54,406 Using built-in specs. 2023-09-12T11:02:54,407 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:54,407 Target: arm-linux-gnueabihf 2023-09-12T11:02:54,408 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:54,408 Thread model: posix 2023-09-12T11:02:54,409 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:54,409 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:54,410 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/exampleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:54,411 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/exampleformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase exampleformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccsyHDvv.s 2023-09-12T11:02:54,419 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:54,420 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:54,421 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:54,422 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:54,422 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:54,423 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:54,423 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:54,424 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:54,425 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:54,425 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:54,426 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:54,427 #include "..." search starts here: 2023-09-12T11:02:54,427 #include <...> search starts here: 2023-09-12T11:02:54,428 /usr/include/eigen3 2023-09-12T11:02:54,429 include 2023-09-12T11:02:54,429 /usr/include/python3.11 2023-09-12T11:02:54,430 /usr/include/c++/12 2023-09-12T11:02:54,430 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:54,431 /usr/include/c++/12/backward 2023-09-12T11:02:54,432 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:54,432 /usr/local/include 2023-09-12T11:02:54,433 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:54,433 /usr/include 2023-09-12T11:02:54,434 End of search list. 2023-09-12T11:02:54,434 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:54,435 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:54,436 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:54,437 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:54,439 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:54,778 ./src/formats/exampleformat.cpp:178:9: warning: "/*" within comment [-Wcomment] 2023-09-12T11:02:54,779 178 | /* Return true if ok. Returning false means discard the OBMol and stop 2023-09-12T11:02:54,780 | 2023-09-12T11:02:56,015 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:56,015 from include/openbabel/mol.h:43, 2023-09-12T11:02:56,016 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:56,017 from ./src/formats/exampleformat.cpp:34: 2023-09-12T11:02:56,018 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:56,018 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:56,019 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:56,019 | ^ 2023-09-12T11:02:56,020 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:56,020 37 | # define UNUSED(x) x 2023-09-12T11:02:56,021 | ^ 2023-09-12T11:02:56,795 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:56,795 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:56,795 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:56,796 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:56,797 | ^ 2023-09-12T11:02:56,797 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:56,798 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:56,798 | ^~~~~~~~ 2023-09-12T11:02:56,800 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:56,801 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:56,802 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:56,802 | ^ 2023-09-12T11:02:56,803 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:56,804 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:56,805 | ^~~~~~~~ 2023-09-12T11:02:56,820 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:56,821 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:56,821 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:56,822 | ^ 2023-09-12T11:02:56,823 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:56,824 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:56,824 | ^~~~~~~~ 2023-09-12T11:02:56,827 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:56,828 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:56,828 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:56,829 | ^ 2023-09-12T11:02:56,830 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:56,831 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:56,831 | ^~~~~~~~ 2023-09-12T11:02:57,001 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:57,001 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:57,002 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:57,003 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:57,003 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:57,004 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:57,004 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:57,005 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:02:57,005 from /usr/include/c++/12/vector:66, 2023-09-12T11:02:57,006 from include/openbabel/mol.h:35: 2023-09-12T11:02:57,006 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:57,007 131 | struct binary_function 2023-09-12T11:02:57,008 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:57,203 ./src/formats/exampleformat.cpp: In member function ‘virtual int OpenBabel::XXXFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:02:57,205 ./src/formats/exampleformat.cpp:128:37: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:02:57,207 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:02:57,208 | ~~~~^ 2023-09-12T11:02:57,210 ./src/formats/exampleformat.cpp:128:54: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:02:57,212 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:02:57,214 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:02:57,216 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:57,218 ./src/formats/exampleformat.cpp:156:12: warning: unused variable ‘ifs’ [-Wunused-variable] 2023-09-12T11:02:57,219 156 | istream& ifs = *pConv->GetInStream(); 2023-09-12T11:02:57,221 | ^~~ 2023-09-12T11:02:57,223 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:57,225 ./src/formats/exampleformat.cpp:203:13: warning: variable ‘levels’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:02:57,227 203 | int levels=0; 2023-09-12T11:02:57,228 | ^~~~~~ 2023-09-12T11:02:58,751 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:58,752 ./src/formats/exampleformat.cpp:171:27: warning: ‘dim’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:58,753 171 | pmol->SetDimension(dim); 2023-09-12T11:02:58,753 | ~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:02:58,754 ./src/formats/exampleformat.cpp:170:13: note: ‘dim’ was declared here 2023-09-12T11:02:58,755 170 | int dim; 2023-09-12T11:02:58,755 | ^~~ 2023-09-12T11:02:59,532 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/exampleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:59,533 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/exampleformat.o /tmp/ccsyHDvv.s 2023-09-12T11:02:59,538 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:59,685 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:02:59,685 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:02:59,686 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/exampleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/exampleformat.' 2023-09-12T11:02:59,687 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/exyzformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/exyzformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:02:59,691 Using built-in specs. 2023-09-12T11:02:59,692 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:59,692 Target: arm-linux-gnueabihf 2023-09-12T11:02:59,693 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:02:59,694 Thread model: posix 2023-09-12T11:02:59,694 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:59,695 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:59,695 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/exyzformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:02:59,696 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/exyzformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase exyzformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cci2GLAe.s 2023-09-12T11:02:59,705 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:59,705 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:59,706 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:59,707 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:59,707 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:59,708 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:59,708 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:59,709 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:59,709 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:59,710 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:59,710 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:59,711 #include "..." search starts here: 2023-09-12T11:02:59,711 #include <...> search starts here: 2023-09-12T11:02:59,712 /usr/include/eigen3 2023-09-12T11:02:59,713 include 2023-09-12T11:02:59,713 /usr/include/python3.11 2023-09-12T11:02:59,714 /usr/include/c++/12 2023-09-12T11:02:59,715 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:59,715 /usr/include/c++/12/backward 2023-09-12T11:02:59,716 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:59,717 /usr/local/include 2023-09-12T11:02:59,717 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:59,718 /usr/include 2023-09-12T11:02:59,719 End of search list. 2023-09-12T11:02:59,719 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:59,720 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:59,721 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:59,721 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:59,723 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:01,304 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:01,305 from include/openbabel/mol.h:43, 2023-09-12T11:03:01,306 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:01,306 from ./src/formats/exyzformat.cpp:18: 2023-09-12T11:03:01,307 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:01,308 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:01,308 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:01,309 | ^ 2023-09-12T11:03:01,310 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:01,310 37 | # define UNUSED(x) x 2023-09-12T11:03:01,311 | ^ 2023-09-12T11:03:02,075 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:02,075 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:02,076 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:02,076 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:02,077 | ^ 2023-09-12T11:03:02,077 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:02,078 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:02,079 | ^~~~~~~~ 2023-09-12T11:03:02,080 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:02,080 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:02,081 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:02,082 | ^ 2023-09-12T11:03:02,082 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:02,083 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:02,083 | ^~~~~~~~ 2023-09-12T11:03:02,099 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:02,099 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:02,100 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:02,101 | ^ 2023-09-12T11:03:02,102 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:02,102 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:02,103 | ^~~~~~~~ 2023-09-12T11:03:02,105 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:02,106 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:02,107 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:02,107 | ^ 2023-09-12T11:03:02,108 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:02,109 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:02,110 | ^~~~~~~~ 2023-09-12T11:03:02,279 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:02,279 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:02,280 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:02,280 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:02,281 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:02,281 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:02,282 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:02,282 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:02,283 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:02,283 from include/openbabel/mol.h:35: 2023-09-12T11:03:02,284 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:02,285 131 | struct binary_function 2023-09-12T11:03:02,285 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:02,627 ./src/formats/exyzformat.cpp: In member function ‘virtual bool OpenBabel::EXYZFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:03:02,628 ./src/formats/exyzformat.cpp:133:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:03:02,629 133 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2023-09-12T11:03:02,629 | ~^ ~~~~~~~ 2023-09-12T11:03:02,630 | | | 2023-09-12T11:03:02,630 | | unsigned int* 2023-09-12T11:03:02,631 | int* 2023-09-12T11:03:02,631 | %d 2023-09-12T11:03:02,708 ./src/formats/exyzformat.cpp:118:19: warning: variable ‘virtualAtoms’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:03:02,709 118 | bool unitCell,virtualAtoms; 2023-09-12T11:03:02,709 | ^~~~~~~~~~~~ 2023-09-12T11:03:08,508 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/exyzformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:08,509 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/exyzformat.o /tmp/cci2GLAe.s 2023-09-12T11:03:08,517 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:08,911 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:03:08,912 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:03:08,913 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/exyzformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/exyzformat.' 2023-09-12T11:03:08,915 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/fastaformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fastaformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:03:08,919 Using built-in specs. 2023-09-12T11:03:08,920 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:08,921 Target: arm-linux-gnueabihf 2023-09-12T11:03:08,921 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:03:08,922 Thread model: posix 2023-09-12T11:03:08,922 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:08,923 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:08,923 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:08,924 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fastaformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase fastaformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccAl9rLv.s 2023-09-12T11:03:08,933 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:08,933 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:08,934 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:08,935 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:08,935 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:08,936 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:08,937 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:08,937 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:08,938 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:08,939 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:08,939 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:08,939 #include "..." search starts here: 2023-09-12T11:03:08,940 #include <...> search starts here: 2023-09-12T11:03:08,940 /usr/include/eigen3 2023-09-12T11:03:08,941 include 2023-09-12T11:03:08,941 /usr/include/python3.11 2023-09-12T11:03:08,941 /usr/include/c++/12 2023-09-12T11:03:08,942 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:08,942 /usr/include/c++/12/backward 2023-09-12T11:03:08,943 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:08,943 /usr/local/include 2023-09-12T11:03:08,944 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:08,944 /usr/include 2023-09-12T11:03:08,944 End of search list. 2023-09-12T11:03:08,945 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:08,945 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:08,946 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:08,947 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:08,953 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:10,581 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:10,581 from include/openbabel/mol.h:43, 2023-09-12T11:03:10,582 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:10,583 from ./src/formats/fastaformat.cpp:21: 2023-09-12T11:03:10,583 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:10,584 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:10,585 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:10,585 | ^ 2023-09-12T11:03:10,586 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:10,587 37 | # define UNUSED(x) x 2023-09-12T11:03:10,588 | ^ 2023-09-12T11:03:11,360 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:11,360 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:11,361 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:11,362 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:11,363 | ^ 2023-09-12T11:03:11,364 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:11,364 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:11,365 | ^~~~~~~~ 2023-09-12T11:03:11,366 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:11,366 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:11,367 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:11,368 | ^ 2023-09-12T11:03:11,369 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:11,370 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:11,370 | ^~~~~~~~ 2023-09-12T11:03:11,385 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:11,386 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:11,386 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:11,387 | ^ 2023-09-12T11:03:11,388 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:11,388 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:11,389 | ^~~~~~~~ 2023-09-12T11:03:11,392 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:11,393 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:11,393 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:11,394 | ^ 2023-09-12T11:03:11,395 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:11,396 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:11,396 | ^~~~~~~~ 2023-09-12T11:03:11,566 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:11,567 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:11,568 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:11,568 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:11,569 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:11,570 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:11,570 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:11,571 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:11,572 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:11,573 from include/openbabel/mol.h:35: 2023-09-12T11:03:11,573 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:11,574 131 | struct binary_function 2023-09-12T11:03:11,575 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:11,841 ./src/formats/fastaformat.cpp: In function ‘void OpenBabel::add_residue(OBMol*, OBResidue*, double, double, long unsigned int&, ResidueRecord*, int, OBAtom*&, bool, bool)’: 2023-09-12T11:03:11,841 ./src/formats/fastaformat.cpp:387:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:03:11,842 387 | else if (atom_count > resBondFromOffset) 2023-09-12T11:03:11,843 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:15,694 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:15,695 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/fastaformat.o /tmp/ccAl9rLv.s 2023-09-12T11:03:15,699 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:16,011 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:03:16,011 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:03:16,012 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastaformat.' 2023-09-12T11:03:16,014 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/fastsearchformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fastsearchformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:03:16,018 Using built-in specs. 2023-09-12T11:03:16,018 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:16,019 Target: arm-linux-gnueabihf 2023-09-12T11:03:16,019 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:03:16,020 Thread model: posix 2023-09-12T11:03:16,021 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:16,022 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:16,022 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastsearchformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:16,023 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fastsearchformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase fastsearchformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccQ9ISp4.s 2023-09-12T11:03:16,032 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:16,032 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:16,033 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:16,034 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:16,034 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:16,035 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:16,035 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:16,036 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:16,036 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:16,037 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:16,038 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:16,038 #include "..." search starts here: 2023-09-12T11:03:16,039 #include <...> search starts here: 2023-09-12T11:03:16,040 /usr/include/eigen3 2023-09-12T11:03:16,040 include 2023-09-12T11:03:16,041 /usr/include/python3.11 2023-09-12T11:03:16,042 /usr/include/c++/12 2023-09-12T11:03:16,042 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:16,043 /usr/include/c++/12/backward 2023-09-12T11:03:16,044 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:16,044 /usr/local/include 2023-09-12T11:03:16,045 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:16,046 /usr/include 2023-09-12T11:03:16,046 End of search list. 2023-09-12T11:03:16,047 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:16,047 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:16,048 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:16,049 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:16,054 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:17,606 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:17,607 from include/openbabel/mol.h:43, 2023-09-12T11:03:17,607 from ./src/formats/fastsearchformat.cpp:20: 2023-09-12T11:03:17,608 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:17,609 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:17,610 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:17,610 | ^ 2023-09-12T11:03:17,611 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:17,612 37 | # define UNUSED(x) x 2023-09-12T11:03:17,612 | ^ 2023-09-12T11:03:18,381 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:18,382 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:18,383 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:18,383 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:18,384 | ^ 2023-09-12T11:03:18,384 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:18,385 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:18,385 | ^~~~~~~~ 2023-09-12T11:03:18,387 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:18,388 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:18,388 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:18,389 | ^ 2023-09-12T11:03:18,389 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:18,390 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:18,391 | ^~~~~~~~ 2023-09-12T11:03:18,406 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:18,407 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:18,408 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:18,408 | ^ 2023-09-12T11:03:18,409 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:18,410 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:18,411 | ^~~~~~~~ 2023-09-12T11:03:18,414 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:18,414 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:18,415 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:18,416 | ^ 2023-09-12T11:03:18,417 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:18,417 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:18,418 | ^~~~~~~~ 2023-09-12T11:03:18,589 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:18,589 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:18,590 from ./src/formats/fastsearchformat.cpp:21: 2023-09-12T11:03:18,591 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:18,591 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:18,592 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:18,592 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:18,593 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:03:18,593 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:03:18,594 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:03:18,594 from /usr/include/c++/12/ios:42, 2023-09-12T11:03:18,595 from /usr/include/c++/12/istream:38, 2023-09-12T11:03:18,595 from /usr/include/c++/12/sstream:38, 2023-09-12T11:03:18,596 from ./src/formats/fastsearchformat.cpp:16: 2023-09-12T11:03:18,596 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:18,597 131 | struct binary_function 2023-09-12T11:03:18,597 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:18,884 ./src/formats/fastsearchformat.cpp: In member function ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’: 2023-09-12T11:03:18,885 ./src/formats/fastsearchformat.cpp:652:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:03:18,885 652 | if(idx>=patternMol.NumBonds()) 2023-09-12T11:03:18,886 | ~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:23,439 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:03:23,440 from include/openbabel/mol.h:35: 2023-09-12T11:03:23,440 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBMol&}; _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’: 2023-09-12T11:03:23,441 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:03:23,442 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:03:23,442 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:23,575 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:03:23,576 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:03:23,577 inlined from ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’ at ./src/formats/fastsearchformat.cpp:657:28: 2023-09-12T11:03:23,577 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:23,578 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:23,578 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:23,579 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:03:23,580 inlined from ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’ at ./src/formats/fastsearchformat.cpp:660:28: 2023-09-12T11:03:23,581 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:23,582 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:23,582 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:23,816 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:03:23,817 inlined from ‘bool OpenBabel::FastSearchFormat::ObtainTarget(OpenBabel::OBConversion*, std::vector&, const std::string&)’ at ./src/formats/fastsearchformat.cpp:606:30: 2023-09-12T11:03:23,817 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:23,818 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:23,819 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:23,819 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:03:23,820 inlined from ‘bool OpenBabel::FastSearchFormat::ObtainTarget(OpenBabel::OBConversion*, std::vector&, const std::string&)’ at ./src/formats/fastsearchformat.cpp:608:32: 2023-09-12T11:03:23,820 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:23,821 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:23,821 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:23,822 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:03:23,823 inlined from ‘bool OpenBabel::FastSearchFormat::ObtainTarget(OpenBabel::OBConversion*, std::vector&, const std::string&)’ at ./src/formats/fastsearchformat.cpp:641:26: 2023-09-12T11:03:23,823 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:23,824 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:23,825 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:24,845 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:03:24,846 inlined from ‘virtual bool OpenBabel::FastSearchFormat::ReadChemObject(OpenBabel::OBConversion*)’ at ./src/formats/fastsearchformat.cpp:212:37: 2023-09-12T11:03:24,847 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:24,847 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:24,848 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:26,497 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastsearchformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:26,498 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/fastsearchformat.o /tmp/ccQ9ISp4.s 2023-09-12T11:03:26,502 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:27,130 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:03:27,131 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:03:27,131 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastsearchformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/fastsearchformat.' 2023-09-12T11:03:27,134 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/fchkformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fchkformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:03:27,138 Using built-in specs. 2023-09-12T11:03:27,139 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:27,140 Target: arm-linux-gnueabihf 2023-09-12T11:03:27,140 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:03:27,141 Thread model: posix 2023-09-12T11:03:27,142 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:27,143 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:27,143 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fchkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:27,144 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fchkformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase fchkformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccEVILtu.s 2023-09-12T11:03:27,151 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:27,152 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:27,153 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:27,154 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:27,154 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:27,155 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:27,155 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:27,155 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:27,156 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:27,156 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:27,157 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:27,157 #include "..." search starts here: 2023-09-12T11:03:27,158 #include <...> search starts here: 2023-09-12T11:03:27,158 /usr/include/eigen3 2023-09-12T11:03:27,159 include 2023-09-12T11:03:27,159 /usr/include/python3.11 2023-09-12T11:03:27,160 /usr/include/c++/12 2023-09-12T11:03:27,160 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:27,161 /usr/include/c++/12/backward 2023-09-12T11:03:27,162 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:27,162 /usr/local/include 2023-09-12T11:03:27,163 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:27,164 /usr/include 2023-09-12T11:03:27,165 End of search list. 2023-09-12T11:03:27,165 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:27,166 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:27,167 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:27,168 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:27,173 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:28,824 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:28,825 from include/openbabel/mol.h:43, 2023-09-12T11:03:28,825 from ./src/formats/fchkformat.cpp:21: 2023-09-12T11:03:28,826 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:28,827 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:28,827 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:28,828 | ^ 2023-09-12T11:03:28,829 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:28,829 37 | # define UNUSED(x) x 2023-09-12T11:03:28,830 | ^ 2023-09-12T11:03:29,599 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:29,600 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,601 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,601 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:29,602 | ^ 2023-09-12T11:03:29,602 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:29,603 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:29,603 | ^~~~~~~~ 2023-09-12T11:03:29,606 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,607 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,607 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:29,608 | ^ 2023-09-12T11:03:29,608 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:29,609 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:29,609 | ^~~~~~~~ 2023-09-12T11:03:29,626 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,627 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,627 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:29,628 | ^ 2023-09-12T11:03:29,629 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:29,629 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:29,630 | ^~~~~~~~ 2023-09-12T11:03:29,634 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,634 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,635 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:29,635 | ^ 2023-09-12T11:03:29,636 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:29,637 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:29,637 | ^~~~~~~~ 2023-09-12T11:03:29,808 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:29,809 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:29,810 from ./src/formats/fchkformat.cpp:22: 2023-09-12T11:03:29,810 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:29,811 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:29,812 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:29,812 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:29,813 In file included from /usr/include/c++/12/functional:49, 2023-09-12T11:03:29,814 from ./src/formats/fchkformat.cpp:16: 2023-09-12T11:03:29,814 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:29,815 131 | struct binary_function 2023-09-12T11:03:29,815 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:30,047 ./src/formats/fchkformat.cpp: In member function ‘virtual bool OpenBabel::FCHKFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:03:30,047 ./src/formats/fchkformat.cpp:587:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:03:30,048 587 | if (alphaorb_found && (numAOrb > alphaorb.size())) 2023-09-12T11:03:30,048 | ~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:03:30,049 ./src/formats/fchkformat.cpp:600:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:03:30,049 600 | if (betaorb_found && (numBOrb > betaorb.size())) 2023-09-12T11:03:30,050 | ~~~~~~~~^~~~~~~~~~~~~~~~ 2023-09-12T11:03:30,055 ./src/formats/fchkformat.cpp:659:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less_equal; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:03:30,056 659 | bind2nd(less_equal(), 0)) || 2023-09-12T11:03:30,056 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:30,057 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T11:03:30,058 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:03:30,058 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:03:30,059 | ^~~~~~~ 2023-09-12T11:03:30,060 ./src/formats/fchkformat.cpp:662:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:03:30,061 662 | bind2nd(greater(), MxBond)) || 2023-09-12T11:03:30,062 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:30,062 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:03:30,063 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:03:30,064 | ^~~~~~~ 2023-09-12T11:03:30,065 ./src/formats/fchkformat.cpp:665:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:03:30,065 665 | bind2nd(less(), 0)) || 2023-09-12T11:03:30,066 | ~~~~~~~^~~~~~~~~~~~~~~~ 2023-09-12T11:03:30,067 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:03:30,067 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:03:30,068 | ^~~~~~~ 2023-09-12T11:03:30,069 ./src/formats/fchkformat.cpp:668:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:03:30,069 668 | bind2nd(greater(), Natoms))) 2023-09-12T11:03:30,070 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:30,071 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:03:30,072 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:03:30,073 | ^~~~~~~ 2023-09-12T11:03:30,073 ./src/formats/fchkformat.cpp:691:40: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:03:30,074 691 | if (numAOrb > 0 && alphaorb.size() == numAOrb) { 2023-09-12T11:03:30,074 | ~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:03:30,076 ./src/formats/fchkformat.cpp:695:41: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:03:30,077 695 | if (numBOrb > 0 && betaorb.size() == numBOrb) { // open shell calculation 2023-09-12T11:03:30,077 | ~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:03:33,901 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:03:33,901 from include/openbabel/mol.h:35: 2023-09-12T11:03:33,902 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:03:33,902 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:03:33,903 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:03:33,904 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:34,015 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:03:34,016 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:03:34,017 inlined from ‘static bool OpenBabel::FCHKFormat::read_numbers(const char*, std::vector<_Tp>&, unsigned int) [with T = double]’ at ./src/formats/fchkformat.cpp:753:26: 2023-09-12T11:03:34,018 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:34,018 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:34,019 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:34,020 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:03:34,021 inlined from ‘static bool OpenBabel::FCHKFormat::read_numbers(const char*, std::vector<_Tp>&, unsigned int) [with T = double]’ at ./src/formats/fchkformat.cpp:775:20: 2023-09-12T11:03:34,021 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:34,022 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:34,023 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:36,443 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:03:36,444 inlined from ‘static bool OpenBabel::FCHKFormat::read_numbers(const char*, std::vector<_Tp>&, unsigned int) [with T = double]’ at ./src/formats/fchkformat.cpp:753:26, 2023-09-12T11:03:36,444 inlined from ‘virtual bool OpenBabel::FCHKFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/fchkformat.cpp:231:42: 2023-09-12T11:03:36,445 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:36,446 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:03:36,447 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:03:39,047 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fchkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:39,048 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/fchkformat.o /tmp/ccEVILtu.s 2023-09-12T11:03:39,052 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:39,716 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:03:39,716 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:03:39,717 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fchkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/fchkformat.' 2023-09-12T11:03:39,720 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/featformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/featformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:03:39,723 Using built-in specs. 2023-09-12T11:03:39,724 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:39,725 Target: arm-linux-gnueabihf 2023-09-12T11:03:39,725 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:03:39,726 Thread model: posix 2023-09-12T11:03:39,727 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:39,727 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:39,728 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/featformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:39,728 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/featformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase featformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccaIytVK.s 2023-09-12T11:03:39,736 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:39,737 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:39,738 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:39,738 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:39,739 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:39,739 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:39,740 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:39,740 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:39,741 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:39,741 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:39,742 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:39,743 #include "..." search starts here: 2023-09-12T11:03:39,743 #include <...> search starts here: 2023-09-12T11:03:39,744 /usr/include/eigen3 2023-09-12T11:03:39,744 include 2023-09-12T11:03:39,745 /usr/include/python3.11 2023-09-12T11:03:39,745 /usr/include/c++/12 2023-09-12T11:03:39,746 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:39,746 /usr/include/c++/12/backward 2023-09-12T11:03:39,747 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:39,747 /usr/local/include 2023-09-12T11:03:39,748 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:39,748 /usr/include 2023-09-12T11:03:39,749 End of search list. 2023-09-12T11:03:39,749 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:39,750 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:39,751 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:39,751 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:39,754 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:41,322 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:41,323 from include/openbabel/mol.h:43, 2023-09-12T11:03:41,323 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:41,324 from ./src/formats/featformat.cpp:17: 2023-09-12T11:03:41,324 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:41,325 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:41,326 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:41,327 | ^ 2023-09-12T11:03:41,327 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:41,328 37 | # define UNUSED(x) x 2023-09-12T11:03:41,328 | ^ 2023-09-12T11:03:42,123 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:42,124 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:42,124 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:42,125 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:42,125 | ^ 2023-09-12T11:03:42,126 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:42,127 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:42,127 | ^~~~~~~~ 2023-09-12T11:03:42,129 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:42,130 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:42,131 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:42,131 | ^ 2023-09-12T11:03:42,132 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:42,133 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:42,133 | ^~~~~~~~ 2023-09-12T11:03:42,150 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:42,150 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:42,151 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:42,152 | ^ 2023-09-12T11:03:42,153 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:42,153 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:42,154 | ^~~~~~~~ 2023-09-12T11:03:42,157 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:42,158 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:42,158 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:42,159 | ^ 2023-09-12T11:03:42,160 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:42,161 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:42,162 | ^~~~~~~~ 2023-09-12T11:03:42,332 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:42,332 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:42,333 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:42,333 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:42,334 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:42,334 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:42,335 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:42,335 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:42,336 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:42,336 from include/openbabel/mol.h:35: 2023-09-12T11:03:42,337 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:42,337 131 | struct binary_function 2023-09-12T11:03:42,338 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:44,909 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/featformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:44,910 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/featformat.o /tmp/ccaIytVK.s 2023-09-12T11:03:44,914 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:45,058 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:03:45,058 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:03:45,059 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/featformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/featformat.' 2023-09-12T11:03:45,059 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/fhformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fhformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:03:45,064 Using built-in specs. 2023-09-12T11:03:45,064 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:45,065 Target: arm-linux-gnueabihf 2023-09-12T11:03:45,065 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:03:45,066 Thread model: posix 2023-09-12T11:03:45,067 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:45,068 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:45,068 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:45,068 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fhformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase fhformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc4Cmyoe.s 2023-09-12T11:03:45,077 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:45,077 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:45,078 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:45,079 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:45,080 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:45,080 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:45,081 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:45,081 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:45,082 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:45,082 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:45,083 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:45,084 #include "..." search starts here: 2023-09-12T11:03:45,084 #include <...> search starts here: 2023-09-12T11:03:45,085 /usr/include/eigen3 2023-09-12T11:03:45,085 include 2023-09-12T11:03:45,086 /usr/include/python3.11 2023-09-12T11:03:45,086 /usr/include/c++/12 2023-09-12T11:03:45,087 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:45,088 /usr/include/c++/12/backward 2023-09-12T11:03:45,088 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:45,089 /usr/local/include 2023-09-12T11:03:45,089 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:45,090 /usr/include 2023-09-12T11:03:45,091 End of search list. 2023-09-12T11:03:45,091 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:45,092 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:45,093 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:45,093 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:45,095 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:46,657 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:46,658 from include/openbabel/mol.h:43, 2023-09-12T11:03:46,658 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:46,659 from ./src/formats/fhformat.cpp:17: 2023-09-12T11:03:46,659 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:46,660 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:46,661 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:46,661 | ^ 2023-09-12T11:03:46,662 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:46,662 37 | # define UNUSED(x) x 2023-09-12T11:03:46,663 | ^ 2023-09-12T11:03:47,426 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:47,426 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,427 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,427 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:47,428 | ^ 2023-09-12T11:03:47,429 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:47,430 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:47,431 | ^~~~~~~~ 2023-09-12T11:03:47,431 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,432 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,433 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:47,433 | ^ 2023-09-12T11:03:47,434 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:47,435 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:47,435 | ^~~~~~~~ 2023-09-12T11:03:47,450 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,450 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,451 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:47,452 | ^ 2023-09-12T11:03:47,453 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:47,454 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:47,455 | ^~~~~~~~ 2023-09-12T11:03:47,456 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,457 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,457 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:47,458 | ^ 2023-09-12T11:03:47,458 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:47,459 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:47,460 | ^~~~~~~~ 2023-09-12T11:03:47,629 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:47,629 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:47,630 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:47,630 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:47,631 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:47,631 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:47,632 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:47,632 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:47,633 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:47,634 from include/openbabel/mol.h:35: 2023-09-12T11:03:47,634 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:47,635 131 | struct binary_function 2023-09-12T11:03:47,636 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:50,193 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:50,194 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/fhformat.o /tmp/cc4Cmyoe.s 2023-09-12T11:03:50,199 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:50,345 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:03:50,345 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:03:50,346 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhformat.' 2023-09-12T11:03:50,347 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/fhiaimsformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fhiaimsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:03:50,351 Using built-in specs. 2023-09-12T11:03:50,352 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:50,352 Target: arm-linux-gnueabihf 2023-09-12T11:03:50,353 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:03:50,353 Thread model: posix 2023-09-12T11:03:50,354 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:50,354 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:50,355 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhiaimsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:50,355 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fhiaimsformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase fhiaimsformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccdCBqst.s 2023-09-12T11:03:50,364 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:50,364 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:50,366 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:50,366 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:50,367 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:50,368 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:50,369 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:50,369 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:50,369 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:50,370 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:50,370 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:50,371 #include "..." search starts here: 2023-09-12T11:03:50,371 #include <...> search starts here: 2023-09-12T11:03:50,371 /usr/include/eigen3 2023-09-12T11:03:50,372 include 2023-09-12T11:03:50,372 /usr/include/python3.11 2023-09-12T11:03:50,373 /usr/include/c++/12 2023-09-12T11:03:50,373 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:50,374 /usr/include/c++/12/backward 2023-09-12T11:03:50,374 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:50,374 /usr/local/include 2023-09-12T11:03:50,375 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:50,375 /usr/include 2023-09-12T11:03:50,376 End of search list. 2023-09-12T11:03:50,376 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:50,377 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:50,378 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:50,378 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:50,382 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:51,952 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:51,953 from include/openbabel/mol.h:43, 2023-09-12T11:03:51,954 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:51,955 from ./src/formats/fhiaimsformat.cpp:15: 2023-09-12T11:03:51,955 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:51,956 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:51,957 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:51,958 | ^ 2023-09-12T11:03:51,958 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:51,959 37 | # define UNUSED(x) x 2023-09-12T11:03:51,960 | ^ 2023-09-12T11:03:52,723 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:52,723 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:52,724 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:52,725 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:52,725 | ^ 2023-09-12T11:03:52,726 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:52,727 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:52,727 | ^~~~~~~~ 2023-09-12T11:03:52,728 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:52,729 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:52,730 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:52,731 | ^ 2023-09-12T11:03:52,731 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:52,732 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:52,732 | ^~~~~~~~ 2023-09-12T11:03:52,747 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:52,747 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:52,748 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:52,749 | ^ 2023-09-12T11:03:52,749 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:52,750 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:52,750 | ^~~~~~~~ 2023-09-12T11:03:52,753 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:52,754 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:52,754 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:52,755 | ^ 2023-09-12T11:03:52,756 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:52,757 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:52,757 | ^~~~~~~~ 2023-09-12T11:03:52,926 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:52,927 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:52,928 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:52,929 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:52,930 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:52,931 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:52,931 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:52,932 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:52,933 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:52,934 from include/openbabel/mol.h:35: 2023-09-12T11:03:52,935 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:52,936 131 | struct binary_function 2023-09-12T11:03:52,936 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:55,521 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:03:55,522 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:03:55,523 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:03:55,524 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:03:55,524 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:55,642 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:03:55,643 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:03:55,643 inlined from ‘virtual bool OpenBabel::FHIaimsFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/fhiaimsformat.cpp:110:26: 2023-09-12T11:03:55,644 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:03:55,645 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:03:55,645 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:55,932 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhiaimsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:55,933 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/fhiaimsformat.o /tmp/ccdCBqst.s 2023-09-12T11:03:55,937 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:56,125 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:03:56,126 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:03:56,126 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhiaimsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/fhiaimsformat.' 2023-09-12T11:03:56,128 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/fingerprintformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fingerprintformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:03:56,132 Using built-in specs. 2023-09-12T11:03:56,132 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:56,133 Target: arm-linux-gnueabihf 2023-09-12T11:03:56,134 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:03:56,135 Thread model: posix 2023-09-12T11:03:56,135 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:56,135 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:56,136 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fingerprintformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:03:56,137 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fingerprintformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase fingerprintformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccZToErK.s 2023-09-12T11:03:56,145 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:56,146 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:56,147 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:56,148 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:56,148 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:56,149 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:56,149 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:56,150 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:56,150 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:56,151 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:56,151 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:56,152 #include "..." search starts here: 2023-09-12T11:03:56,153 #include <...> search starts here: 2023-09-12T11:03:56,153 /usr/include/eigen3 2023-09-12T11:03:56,154 include 2023-09-12T11:03:56,154 /usr/include/python3.11 2023-09-12T11:03:56,155 /usr/include/c++/12 2023-09-12T11:03:56,155 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:56,156 /usr/include/c++/12/backward 2023-09-12T11:03:56,157 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:56,157 /usr/local/include 2023-09-12T11:03:56,158 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:56,159 /usr/include 2023-09-12T11:03:56,159 End of search list. 2023-09-12T11:03:56,159 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:56,160 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:56,161 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:56,161 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:56,167 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:57,882 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:57,882 from include/openbabel/mol.h:43, 2023-09-12T11:03:57,883 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:57,884 from ./src/formats/fingerprintformat.cpp:19: 2023-09-12T11:03:57,884 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:57,885 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:57,885 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:57,886 | ^ 2023-09-12T11:03:57,886 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:57,887 37 | # define UNUSED(x) x 2023-09-12T11:03:57,888 | ^ 2023-09-12T11:03:58,654 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:58,655 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:58,656 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:58,656 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:58,657 | ^ 2023-09-12T11:03:58,658 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:58,658 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:58,659 | ^~~~~~~~ 2023-09-12T11:03:58,660 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:58,661 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:58,661 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:58,662 | ^ 2023-09-12T11:03:58,663 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:58,664 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:58,664 | ^~~~~~~~ 2023-09-12T11:03:58,680 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:58,680 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:58,681 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:58,682 | ^ 2023-09-12T11:03:58,683 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:58,684 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:58,684 | ^~~~~~~~ 2023-09-12T11:03:58,687 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:58,687 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:58,688 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:58,689 | ^ 2023-09-12T11:03:58,689 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:58,690 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:58,690 | ^~~~~~~~ 2023-09-12T11:03:58,860 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:58,861 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:58,862 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:58,862 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:58,863 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:58,864 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:58,864 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:58,865 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:58,866 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:58,866 from ./src/formats/fingerprintformat.cpp:15: 2023-09-12T11:03:58,867 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:58,868 131 | struct binary_function 2023-09-12T11:03:58,868 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:02,624 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fingerprintformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:02,625 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/fingerprintformat.o /tmp/ccZToErK.s 2023-09-12T11:04:02,630 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:02,895 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:04:02,895 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:04:02,896 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fingerprintformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/fingerprintformat.' 2023-09-12T11:04:02,898 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/fpsformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fpsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:04:02,901 Using built-in specs. 2023-09-12T11:04:02,902 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:02,902 Target: arm-linux-gnueabihf 2023-09-12T11:04:02,903 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:04:02,903 Thread model: posix 2023-09-12T11:04:02,904 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:02,904 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:02,905 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fpsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:02,905 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fpsformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase fpsformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccw3snR0.s 2023-09-12T11:04:02,914 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:02,915 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:02,916 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:02,916 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:02,917 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:02,918 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:02,918 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:02,918 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:02,919 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:02,919 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:02,920 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:02,920 #include "..." search starts here: 2023-09-12T11:04:02,921 #include <...> search starts here: 2023-09-12T11:04:02,921 /usr/include/eigen3 2023-09-12T11:04:02,921 include 2023-09-12T11:04:02,922 /usr/include/python3.11 2023-09-12T11:04:02,922 /usr/include/c++/12 2023-09-12T11:04:02,923 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:02,923 /usr/include/c++/12/backward 2023-09-12T11:04:02,924 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:02,924 /usr/local/include 2023-09-12T11:04:02,924 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:02,925 /usr/include 2023-09-12T11:04:02,925 End of search list. 2023-09-12T11:04:02,926 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:02,926 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:02,927 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:02,928 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:02,934 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:04,635 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:04,635 from include/openbabel/mol.h:43, 2023-09-12T11:04:04,636 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:04,636 from ./src/formats/fpsformat.cpp:19: 2023-09-12T11:04:04,637 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:04,638 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:04,638 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:04,639 | ^ 2023-09-12T11:04:04,640 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:04,640 37 | # define UNUSED(x) x 2023-09-12T11:04:04,641 | ^ 2023-09-12T11:04:05,411 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:05,412 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:05,413 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:05,413 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:05,414 | ^ 2023-09-12T11:04:05,415 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:05,415 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:05,416 | ^~~~~~~~ 2023-09-12T11:04:05,417 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:05,418 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:05,418 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:05,419 | ^ 2023-09-12T11:04:05,419 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:05,420 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:05,420 | ^~~~~~~~ 2023-09-12T11:04:05,436 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:05,437 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:05,438 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:05,438 | ^ 2023-09-12T11:04:05,439 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:05,439 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:05,440 | ^~~~~~~~ 2023-09-12T11:04:05,443 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:05,444 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:05,444 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:05,445 | ^ 2023-09-12T11:04:05,446 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:05,446 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:05,447 | ^~~~~~~~ 2023-09-12T11:04:05,616 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:05,617 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:05,618 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:05,618 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:05,619 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:05,620 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:05,620 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:05,621 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:05,622 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:05,622 from ./src/formats/fpsformat.cpp:15: 2023-09-12T11:04:05,623 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:05,624 131 | struct binary_function 2023-09-12T11:04:05,625 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:05,844 ./src/formats/fpsformat.cpp: In member function ‘virtual bool OpenBabel::FPSFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:05,844 ./src/formats/fpsformat.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:04:05,845 146 | for(unsigned i=0;i<(_nbits+31)/32;++i) 2023-09-12T11:04:05,846 | ~^~~~~~~~~~~~~~~ 2023-09-12T11:04:05,852 ./src/formats/fpsformat.cpp: In member function ‘std::string OpenBabel::FPSFormat::getTimeStr()’: 2023-09-12T11:04:05,852 ./src/formats/fpsformat.cpp:169:10: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:04:05,853 169 | size_t time_res; /* Result of strftime */ 2023-09-12T11:04:05,854 | ^~~~~~~~ 2023-09-12T11:04:09,190 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fpsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:09,191 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/fpsformat.o /tmp/ccw3snR0.s 2023-09-12T11:04:09,198 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:09,436 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:04:09,437 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:04:09,437 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/fpsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/fpsformat.' 2023-09-12T11:04:09,439 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/freefracformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/freefracformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:04:09,443 Using built-in specs. 2023-09-12T11:04:09,444 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:09,444 Target: arm-linux-gnueabihf 2023-09-12T11:04:09,445 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:04:09,446 Thread model: posix 2023-09-12T11:04:09,447 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:09,447 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:09,447 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/freefracformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:09,448 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/freefracformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase freefracformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc6y2RSe.s 2023-09-12T11:04:09,457 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:09,457 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:09,458 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:09,459 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:09,460 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:09,460 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:09,461 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:09,461 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:09,462 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:09,463 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:09,463 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:09,464 #include "..." search starts here: 2023-09-12T11:04:09,464 #include <...> search starts here: 2023-09-12T11:04:09,465 /usr/include/eigen3 2023-09-12T11:04:09,465 include 2023-09-12T11:04:09,466 /usr/include/python3.11 2023-09-12T11:04:09,467 /usr/include/c++/12 2023-09-12T11:04:09,467 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:09,468 /usr/include/c++/12/backward 2023-09-12T11:04:09,468 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:09,469 /usr/local/include 2023-09-12T11:04:09,470 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:09,470 /usr/include 2023-09-12T11:04:09,471 End of search list. 2023-09-12T11:04:09,471 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:09,472 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:09,473 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:09,474 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:09,475 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:11,045 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:11,046 from include/openbabel/mol.h:43, 2023-09-12T11:04:11,046 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:11,047 from ./src/formats/freefracformat.cpp:16: 2023-09-12T11:04:11,047 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:11,048 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:11,048 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:11,049 | ^ 2023-09-12T11:04:11,049 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:11,050 37 | # define UNUSED(x) x 2023-09-12T11:04:11,050 | ^ 2023-09-12T11:04:11,814 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:11,815 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:11,815 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:11,816 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:11,817 | ^ 2023-09-12T11:04:11,817 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:11,818 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:11,819 | ^~~~~~~~ 2023-09-12T11:04:11,819 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:11,820 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:11,821 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:11,821 | ^ 2023-09-12T11:04:11,822 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:11,823 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:11,823 | ^~~~~~~~ 2023-09-12T11:04:11,838 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:11,839 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:11,840 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:11,840 | ^ 2023-09-12T11:04:11,841 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:11,842 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:11,842 | ^~~~~~~~ 2023-09-12T11:04:11,845 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:11,845 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:11,846 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:11,847 | ^ 2023-09-12T11:04:11,847 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:11,848 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:11,848 | ^~~~~~~~ 2023-09-12T11:04:12,018 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:12,018 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:12,019 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:12,019 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:12,020 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:12,020 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:12,021 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:12,022 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:12,022 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:12,023 from include/openbabel/mol.h:35: 2023-09-12T11:04:12,024 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:12,024 131 | struct binary_function 2023-09-12T11:04:12,025 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:15,022 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/freefracformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:15,023 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/freefracformat.o /tmp/cc6y2RSe.s 2023-09-12T11:04:15,027 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:15,234 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:04:15,235 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:04:15,235 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/freefracformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/freefracformat.' 2023-09-12T11:04:15,237 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/gamessformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/gamessformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:04:15,241 Using built-in specs. 2023-09-12T11:04:15,243 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:15,243 Target: arm-linux-gnueabihf 2023-09-12T11:04:15,244 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:04:15,244 Thread model: posix 2023-09-12T11:04:15,245 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:15,246 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:15,246 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:15,247 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gamessformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase gamessformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccCMxmBI.s 2023-09-12T11:04:15,257 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:15,258 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:15,259 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:15,260 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:15,260 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:15,261 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:15,262 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:15,262 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:15,263 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:15,264 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:15,264 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:15,265 #include "..." search starts here: 2023-09-12T11:04:15,265 #include <...> search starts here: 2023-09-12T11:04:15,265 /usr/include/eigen3 2023-09-12T11:04:15,266 include 2023-09-12T11:04:15,266 /usr/include/python3.11 2023-09-12T11:04:15,267 /usr/include/c++/12 2023-09-12T11:04:15,267 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:15,268 /usr/include/c++/12/backward 2023-09-12T11:04:15,268 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:15,269 /usr/local/include 2023-09-12T11:04:15,269 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:15,269 /usr/include 2023-09-12T11:04:15,270 End of search list. 2023-09-12T11:04:15,270 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:15,271 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:15,272 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:15,272 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:15,276 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:16,849 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:16,850 from include/openbabel/mol.h:43, 2023-09-12T11:04:16,850 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:16,851 from ./src/formats/gamessformat.cpp:19: 2023-09-12T11:04:16,851 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:16,852 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:16,852 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:16,853 | ^ 2023-09-12T11:04:16,854 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:16,854 37 | # define UNUSED(x) x 2023-09-12T11:04:16,855 | ^ 2023-09-12T11:04:17,619 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:17,620 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:17,620 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:17,621 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:17,622 | ^ 2023-09-12T11:04:17,622 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:17,623 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:17,624 | ^~~~~~~~ 2023-09-12T11:04:17,624 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:17,625 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:17,626 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:17,627 | ^ 2023-09-12T11:04:17,627 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:17,628 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:17,629 | ^~~~~~~~ 2023-09-12T11:04:17,643 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:17,644 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:17,645 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:17,645 | ^ 2023-09-12T11:04:17,646 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:17,646 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:17,647 | ^~~~~~~~ 2023-09-12T11:04:17,650 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:17,650 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:17,651 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:17,652 | ^ 2023-09-12T11:04:17,652 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:17,653 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:17,653 | ^~~~~~~~ 2023-09-12T11:04:17,823 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:17,823 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:17,824 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:17,825 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:17,826 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:17,827 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:17,827 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:17,828 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:17,829 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:17,830 from include/openbabel/mol.h:35: 2023-09-12T11:04:17,830 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:17,831 131 | struct binary_function 2023-09-12T11:04:17,832 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:18,097 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:18,097 ./src/formats/gamessformat.cpp:227:9: warning: variable ‘ndummyatoms’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:04:18,098 227 | int ndummyatoms = 0; 2023-09-12T11:04:18,099 | ^~~~~~~~~~~ 2023-09-12T11:04:18,117 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:18,118 ./src/formats/gamessformat.cpp:995:14: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 2023-09-12T11:04:18,119 995 | static const bool cmpfn(const char& a, const char& b) { 2023-09-12T11:04:18,120 | ^~~~~ 2023-09-12T11:04:23,195 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:04:23,196 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:04:23,197 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:23,197 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:04:23,197 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:23,348 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:04:23,348 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:23,408 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:04:23,409 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:27,334 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:27,334 ./src/formats/gamessformat.cpp:520:58: warning: ‘lowFreqModesEnd’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:04:27,335 520 | if (numIntens < lowFreqModesBegin || numIntens > lowFreqModesEnd) 2023-09-12T11:04:27,336 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,336 ./src/formats/gamessformat.cpp:239:9: note: ‘lowFreqModesEnd’ was declared here 2023-09-12T11:04:27,337 239 | int lowFreqModesEnd; // the number of the last low frequency mode 2023-09-12T11:04:27,338 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:27,339 ./src/formats/gamessformat.cpp:520:25: warning: ‘lowFreqModesBegin’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:04:27,340 520 | if (numIntens < lowFreqModesBegin || numIntens > lowFreqModesEnd) 2023-09-12T11:04:27,340 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,341 ./src/formats/gamessformat.cpp:238:9: note: ‘lowFreqModesBegin’ was declared here 2023-09-12T11:04:27,342 238 | int lowFreqModesBegin; // the number of the first low frequency mode 2023-09-12T11:04:27,342 | ^~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,429 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:04:27,430 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,430 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:279:31: 2023-09-12T11:04:27,431 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,432 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,433 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,433 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,434 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:280:31: 2023-09-12T11:04:27,435 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,436 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,436 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,437 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,437 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:281:31: 2023-09-12T11:04:27,438 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,438 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,439 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,439 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,440 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:302:32: 2023-09-12T11:04:27,440 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,441 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,442 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,443 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,443 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:324:34: 2023-09-12T11:04:27,444 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,445 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,446 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,446 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,447 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:325:34: 2023-09-12T11:04:27,451 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,452 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,453 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,453 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,454 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:326:34: 2023-09-12T11:04:27,455 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,455 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,456 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,457 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,458 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:332:34: 2023-09-12T11:04:27,458 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,459 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,459 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,460 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,460 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:333:34: 2023-09-12T11:04:27,461 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,461 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,462 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,462 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,463 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:334:34: 2023-09-12T11:04:27,464 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,464 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,465 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,466 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,467 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:363:32: 2023-09-12T11:04:27,467 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,468 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,469 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,470 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,470 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:364:32: 2023-09-12T11:04:27,471 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,471 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,472 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,473 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,474 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:365:32: 2023-09-12T11:04:27,474 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,475 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,476 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,477 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,477 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:400:36: 2023-09-12T11:04:27,478 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,478 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,479 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,479 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,480 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:401:36: 2023-09-12T11:04:27,481 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,481 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,482 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,483 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,483 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:402:36: 2023-09-12T11:04:27,484 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,485 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:27,485 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:27,486 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,487 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,488 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:429:35: 2023-09-12T11:04:27,489 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,489 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,490 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,490 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,491 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,492 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:511:34: 2023-09-12T11:04:27,493 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,493 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,495 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,495 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,496 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,496 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:513:34: 2023-09-12T11:04:27,497 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,497 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,498 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,498 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,499 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,499 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:521:34: 2023-09-12T11:04:27,500 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,500 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,501 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,502 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,503 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,503 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:528:42: 2023-09-12T11:04:27,504 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,505 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,506 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,506 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,507 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,507 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:555:24: 2023-09-12T11:04:27,508 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,509 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,510 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,511 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,511 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,512 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:561:24: 2023-09-12T11:04:27,513 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,513 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,514 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,515 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,515 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,516 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:568:24: 2023-09-12T11:04:27,517 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,518 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,519 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,520 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:27,521 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,521 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:576:51: 2023-09-12T11:04:27,522 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,523 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,524 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:27,525 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:27,526 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:27,526 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:602:31: 2023-09-12T11:04:27,527 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:27,528 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:27,529 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:32,491 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:32,492 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/gamessformat.o /tmp/ccCMxmBI.s 2023-09-12T11:04:32,496 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:33,477 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:04:33,477 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:04:33,478 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessformat.' 2023-09-12T11:04:33,482 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/gamessukformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/gamessukformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:04:33,486 Using built-in specs. 2023-09-12T11:04:33,487 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:33,487 Target: arm-linux-gnueabihf 2023-09-12T11:04:33,488 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:04:33,489 Thread model: posix 2023-09-12T11:04:33,489 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:33,490 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:33,490 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessukformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:33,491 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gamessukformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase gamessukformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccNKkU0n.s 2023-09-12T11:04:33,500 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:33,500 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:33,501 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:33,502 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:33,502 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:33,503 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:33,503 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:33,504 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:33,505 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:33,505 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:33,506 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:33,507 #include "..." search starts here: 2023-09-12T11:04:33,507 #include <...> search starts here: 2023-09-12T11:04:33,508 /usr/include/eigen3 2023-09-12T11:04:33,508 include 2023-09-12T11:04:33,509 /usr/include/python3.11 2023-09-12T11:04:33,510 /usr/include/c++/12 2023-09-12T11:04:33,510 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:33,511 /usr/include/c++/12/backward 2023-09-12T11:04:33,512 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:33,512 /usr/local/include 2023-09-12T11:04:33,513 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:33,514 /usr/include 2023-09-12T11:04:33,514 End of search list. 2023-09-12T11:04:33,515 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:33,515 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:33,516 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:33,517 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:33,518 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:35,097 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:35,097 from include/openbabel/mol.h:43, 2023-09-12T11:04:35,098 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:35,099 from ./src/formats/gamessukformat.cpp:14: 2023-09-12T11:04:35,099 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:35,100 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:35,101 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:35,101 | ^ 2023-09-12T11:04:35,102 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:35,103 37 | # define UNUSED(x) x 2023-09-12T11:04:35,104 | ^ 2023-09-12T11:04:35,868 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:35,869 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:35,869 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:35,870 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:35,870 | ^ 2023-09-12T11:04:35,871 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:35,871 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:35,872 | ^~~~~~~~ 2023-09-12T11:04:35,874 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:35,875 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:35,876 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:35,876 | ^ 2023-09-12T11:04:35,877 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:35,878 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:35,878 | ^~~~~~~~ 2023-09-12T11:04:35,894 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:35,895 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:35,896 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:35,897 | ^ 2023-09-12T11:04:35,898 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:35,898 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:35,899 | ^~~~~~~~ 2023-09-12T11:04:35,902 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:35,903 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:35,903 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:35,904 | ^ 2023-09-12T11:04:35,905 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:35,905 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:35,906 | ^~~~~~~~ 2023-09-12T11:04:36,077 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:36,077 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:36,078 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:36,078 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:36,079 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:36,079 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:36,080 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:36,081 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:36,081 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:36,082 from include/openbabel/mol.h:35: 2023-09-12T11:04:36,082 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:36,083 131 | struct binary_function 2023-09-12T11:04:36,083 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:36,342 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’: 2023-09-12T11:04:36,342 ./src/formats/gamessukformat.cpp:307:97: warning: unused parameter ‘factor’ [-Wunused-parameter] 2023-09-12T11:04:36,343 307 | bool GAMESSUKFormat::ReadLineZmatrix(OBMol &mol, OBAtom *atom, vector &tokens, double factor, int *zmatLineCount) 2023-09-12T11:04:36,344 | ~~~~~~~^~~~~~ 2023-09-12T11:04:36,390 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadInitialCartesian(OpenBabel::OBMol&, std::istream&)’: 2023-09-12T11:04:36,390 ./src/formats/gamessukformat.cpp:779:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:04:36,391 779 | bool ok=false; 2023-09-12T11:04:36,392 | ^~ 2023-09-12T11:04:36,394 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz1(OpenBabel::OBMol&, std::istream&)’: 2023-09-12T11:04:36,395 ./src/formats/gamessukformat.cpp:845:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:04:36,395 845 | bool ok=false; 2023-09-12T11:04:36,396 | ^~ 2023-09-12T11:04:36,398 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz2(OpenBabel::OBMol&, std::istream&)’: 2023-09-12T11:04:36,399 ./src/formats/gamessukformat.cpp:892:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:04:36,399 892 | bool ok=false; 2023-09-12T11:04:36,400 | ^~ 2023-09-12T11:04:36,431 ./src/formats/gamessukformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSUKOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:36,432 ./src/formats/gamessukformat.cpp:1207:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:04:36,433 1207 | bool ok; 2023-09-12T11:04:36,433 | ^~ 2023-09-12T11:04:43,063 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:04:43,063 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:04:43,064 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:43,065 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:04:43,066 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:43,286 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:04:43,286 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:43,347 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:04:43,348 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:44,117 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:44,117 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:44,118 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesHessian(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:955:30: 2023-09-12T11:04:44,118 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:44,119 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:44,120 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:44,122 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:04:44,123 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:44,123 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesHessian(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:976:36: 2023-09-12T11:04:44,124 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:44,125 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:44,126 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:44,127 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:44,127 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:44,128 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesHessian(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:977:36: 2023-09-12T11:04:44,128 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:44,129 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:44,130 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:45,085 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:45,085 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:45,086 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesForce(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:1075:30: 2023-09-12T11:04:45,087 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:45,088 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:45,088 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:45,090 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:45,091 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesForce(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:1099:36: 2023-09-12T11:04:45,091 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:45,092 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:45,092 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:04:45,093 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:45,094 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:45,094 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesForce(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:1100:36: 2023-09-12T11:04:45,095 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:45,095 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:45,096 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:45,854 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:04:45,854 from include/openbabel/mol.h:37: 2023-09-12T11:04:45,855 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:04:45,856 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:04:45,857 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:04:45,857 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:45,966 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:04:45,966 /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:04:45,967 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:04:45,968 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:45,968 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:45,969 512 | std::tuple(__k), 2023-09-12T11:04:45,969 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:45,970 513 | std::tuple<>()); 2023-09-12T11:04:45,970 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,103 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:04:46,104 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadVariables(std::istream&, double, std::string)’ at ./src/formats/gamessukformat.cpp:472:26: 2023-09-12T11:04:46,105 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:04:46,105 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:46,106 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,107 512 | std::tuple(__k), 2023-09-12T11:04:46,108 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,108 513 | std::tuple<>()); 2023-09-12T11:04:46,109 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,514 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:04:46,514 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:280:32: 2023-09-12T11:04:46,515 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:04:46,516 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:46,517 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,517 512 | std::tuple(__k), 2023-09-12T11:04:46,518 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,518 513 | std::tuple<>()); 2023-09-12T11:04:46,519 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,519 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:04:46,520 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:288:32: 2023-09-12T11:04:46,521 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:04:46,521 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:46,522 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,522 512 | std::tuple(__k), 2023-09-12T11:04:46,523 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,524 513 | std::tuple<>()); 2023-09-12T11:04:46,524 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,525 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:04:46,526 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:296:32: 2023-09-12T11:04:46,527 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:04:46,527 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:46,528 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,529 512 | std::tuple(__k), 2023-09-12T11:04:46,529 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:46,530 513 | std::tuple<>()); 2023-09-12T11:04:46,531 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:47,009 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:04:47,010 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:386:36: 2023-09-12T11:04:47,011 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:04:47,011 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:47,012 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:47,012 512 | std::tuple(__k), 2023-09-12T11:04:47,013 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:47,013 513 | std::tuple<>()); 2023-09-12T11:04:47,014 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:48,824 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessukformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:48,825 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/gamessukformat.o /tmp/ccNKkU0n.s 2023-09-12T11:04:48,829 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:49,887 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:04:49,888 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:04:49,888 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessukformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/gamessukformat.' 2023-09-12T11:04:49,893 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/gausscubeformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/gausscubeformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:04:49,897 Using built-in specs. 2023-09-12T11:04:49,897 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:49,898 Target: arm-linux-gnueabihf 2023-09-12T11:04:49,898 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:04:49,899 Thread model: posix 2023-09-12T11:04:49,899 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:49,900 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:49,900 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausscubeformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:04:49,901 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gausscubeformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase gausscubeformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccvYofyZ.s 2023-09-12T11:04:49,909 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:49,910 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:49,911 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:49,912 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:49,912 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:49,913 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:49,913 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:49,914 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:49,914 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:49,915 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:49,915 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:49,916 #include "..." search starts here: 2023-09-12T11:04:49,916 #include <...> search starts here: 2023-09-12T11:04:49,917 /usr/include/eigen3 2023-09-12T11:04:49,918 include 2023-09-12T11:04:49,918 /usr/include/python3.11 2023-09-12T11:04:49,918 /usr/include/c++/12 2023-09-12T11:04:49,919 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:49,919 /usr/include/c++/12/backward 2023-09-12T11:04:49,920 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:49,920 /usr/local/include 2023-09-12T11:04:49,921 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:49,921 /usr/include 2023-09-12T11:04:49,921 End of search list. 2023-09-12T11:04:49,922 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:49,922 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:49,923 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:49,924 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:49,927 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:51,496 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:51,496 from include/openbabel/mol.h:43, 2023-09-12T11:04:51,497 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:51,497 from ./src/formats/gausscubeformat.cpp:28: 2023-09-12T11:04:51,498 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:51,498 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:51,499 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:51,500 | ^ 2023-09-12T11:04:51,500 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:51,501 37 | # define UNUSED(x) x 2023-09-12T11:04:51,502 | ^ 2023-09-12T11:04:52,270 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:52,271 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:52,272 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:52,273 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:52,274 | ^ 2023-09-12T11:04:52,275 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:52,276 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:52,277 | ^~~~~~~~ 2023-09-12T11:04:52,278 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:52,278 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:52,279 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:52,281 | ^ 2023-09-12T11:04:52,282 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:52,283 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:52,283 | ^~~~~~~~ 2023-09-12T11:04:52,295 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:52,296 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:52,300 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:52,301 | ^ 2023-09-12T11:04:52,304 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:52,305 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:52,305 | ^~~~~~~~ 2023-09-12T11:04:52,306 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:52,307 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:52,308 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:52,309 | ^ 2023-09-12T11:04:52,309 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:52,310 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:52,311 | ^~~~~~~~ 2023-09-12T11:04:52,476 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:52,477 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:52,478 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:52,478 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:52,479 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:52,480 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:52,481 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:52,482 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:04:52,483 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:04:52,484 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:04:52,485 from /usr/include/c++/12/ios:42, 2023-09-12T11:04:52,486 from /usr/include/c++/12/istream:38, 2023-09-12T11:04:52,487 from /usr/include/c++/12/sstream:38, 2023-09-12T11:04:52,488 from ./src/formats/gausscubeformat.cpp:25: 2023-09-12T11:04:52,488 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:52,489 131 | struct binary_function 2023-09-12T11:04:52,490 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:52,684 ./src/formats/gausscubeformat.cpp: In member function ‘virtual int OpenBabel::OBGaussianCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:04:52,685 ./src/formats/gausscubeformat.cpp:79:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:04:52,686 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:04:52,687 | ~~~~^ 2023-09-12T11:04:52,688 ./src/formats/gausscubeformat.cpp:79:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:52,688 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:04:52,689 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:52,768 ./src/formats/gausscubeformat.cpp: In member function ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:52,768 ./src/formats/gausscubeformat.cpp:425:25: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:04:52,769 425 | while (vgd.size() < nCubes) 2023-09-12T11:04:52,770 | ~~~~~~~~~~~^~~~~~~~ 2023-09-12T11:04:52,778 ./src/formats/gausscubeformat.cpp:472:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:04:52,779 472 | while (values.size() < n*nCubes) 2023-09-12T11:04:52,780 | ~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:04:52,801 ./src/formats/gausscubeformat.cpp:107:17: warning: unused variable ‘title’ [-Wunused-variable] 2023-09-12T11:04:52,802 107 | const char* title = pConv->GetTitle(); 2023-09-12T11:04:52,803 | ^~~~~ 2023-09-12T11:04:56,611 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:04:56,611 from include/openbabel/mol.h:35: 2023-09-12T11:04:56,612 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:04:56,612 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:56,613 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:04:56,614 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:56,712 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:04:56,712 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:58,167 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:58,167 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:04:58,168 inlined from ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gausscubeformat.cpp:500:25: 2023-09-12T11:04:58,169 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:58,169 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:58,170 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:58,171 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:04:58,171 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:04:58,172 inlined from ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gausscubeformat.cpp:511:25: 2023-09-12T11:04:58,173 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:04:58,174 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:04:58,174 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:01,440 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausscubeformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:01,441 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/gausscubeformat.o /tmp/ccvYofyZ.s 2023-09-12T11:05:01,446 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:02,098 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:05:02,099 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:05:02,099 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausscubeformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausscubeformat.' 2023-09-12T11:05:02,102 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/gaussformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/gaussformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:05:02,106 Using built-in specs. 2023-09-12T11:05:02,107 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:02,108 Target: arm-linux-gnueabihf 2023-09-12T11:05:02,108 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:05:02,109 Thread model: posix 2023-09-12T11:05:02,110 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:02,111 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:02,111 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gaussformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:02,113 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gaussformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase gaussformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccOoMhPS.s 2023-09-12T11:05:02,119 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:02,120 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:02,121 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:02,122 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:02,122 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:02,122 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:02,123 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:02,124 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:02,124 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:02,125 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:02,125 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:02,126 #include "..." search starts here: 2023-09-12T11:05:02,126 #include <...> search starts here: 2023-09-12T11:05:02,127 /usr/include/eigen3 2023-09-12T11:05:02,128 include 2023-09-12T11:05:02,128 /usr/include/python3.11 2023-09-12T11:05:02,129 /usr/include/c++/12 2023-09-12T11:05:02,129 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:02,130 /usr/include/c++/12/backward 2023-09-12T11:05:02,131 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:02,131 /usr/local/include 2023-09-12T11:05:02,132 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:02,132 /usr/include 2023-09-12T11:05:02,133 End of search list. 2023-09-12T11:05:02,133 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:02,138 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:02,139 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:02,139 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:02,141 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:04,070 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:04,071 from include/openbabel/mol.h:43, 2023-09-12T11:05:04,071 from include/openbabel/data_utilities.h:25, 2023-09-12T11:05:04,072 from ./src/formats/gaussformat.cpp:18: 2023-09-12T11:05:04,073 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:04,074 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:04,074 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:04,076 | ^ 2023-09-12T11:05:04,076 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:04,077 37 | # define UNUSED(x) x 2023-09-12T11:05:04,077 | ^ 2023-09-12T11:05:04,743 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:04,743 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:04,744 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:04,745 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:04,745 | ^ 2023-09-12T11:05:04,746 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:04,746 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:04,747 | ^~~~~~~~ 2023-09-12T11:05:04,748 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:04,748 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:04,749 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:04,750 | ^ 2023-09-12T11:05:04,751 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:04,751 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:04,752 | ^~~~~~~~ 2023-09-12T11:05:04,767 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:04,768 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:04,768 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:04,769 | ^ 2023-09-12T11:05:04,770 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:04,770 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:04,771 | ^~~~~~~~ 2023-09-12T11:05:04,773 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:04,774 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:04,775 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:04,775 | ^ 2023-09-12T11:05:04,776 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:04,777 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:04,778 | ^~~~~~~~ 2023-09-12T11:05:04,947 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:04,947 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:04,948 from include/openbabel/obmolecformat.h:31, 2023-09-12T11:05:04,949 from ./src/formats/gaussformat.cpp:19: 2023-09-12T11:05:04,949 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:04,950 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:04,950 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:04,951 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:04,951 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:05:04,952 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:05:04,952 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:05:04,953 from /usr/include/c++/12/ios:42, 2023-09-12T11:05:04,954 from /usr/include/c++/12/istream:38, 2023-09-12T11:05:04,954 from /usr/include/c++/12/fstream:38, 2023-09-12T11:05:04,955 from include/openbabel/data.h:27, 2023-09-12T11:05:04,955 from ./src/formats/gaussformat.cpp:17: 2023-09-12T11:05:04,956 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:04,956 131 | struct binary_function 2023-09-12T11:05:04,957 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:05,188 ./src/formats/gaussformat.cpp: In function ‘void OpenBabel::add_unique_pairdata_to_mol(OBMol*, std::string, std::string, int)’: 2023-09-12T11:05:05,189 ./src/formats/gaussformat.cpp:275:19: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:05:05,190 275 | if (vs.size() >= start) 2023-09-12T11:05:05,190 | ~~~~~~~~~~^~~~~~~~ 2023-09-12T11:05:05,191 ./src/formats/gaussformat.cpp:278:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:05:05,192 278 | for(i=start+1; (i)’: 2023-09-12T11:05:05,199 ./src/formats/gaussformat.cpp:332:17: warning: unused variable ‘pg’ [-Wunused-variable] 2023-09-12T11:05:05,199 332 | const char *pg = obPG.IdentifyPointGroup(); 2023-09-12T11:05:05,200 | ^~ 2023-09-12T11:05:11,921 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:05:11,921 from include/openbabel/data.h:28: 2023-09-12T11:05:11,922 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:05:11,923 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:11,923 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:05:11,924 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:11,957 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:05:11,958 /usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:05:11,959 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:11,960 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:11,960 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:12,134 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:05:12,134 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:12,135 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:05:12,136 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:12,169 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:05:12,170 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:12,170 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:12,171 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:12,204 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:05:12,205 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:12,205 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:05:12,206 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,006 ./src/formats/gaussformat.cpp: In member function ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:16,007 ./src/formats/gaussformat.cpp:1164:25: warning: ‘CV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:16,008 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:05:16,009 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,009 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:05:16,010 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,011 ./src/formats/gaussformat.cpp:450:32: note: ‘CV’ was declared here 2023-09-12T11:05:16,012 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:05:16,013 | ^~ 2023-09-12T11:05:16,013 ./src/formats/gaussformat.cpp:1164:25: warning: ‘E0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:16,014 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:05:16,015 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,016 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:05:16,016 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,017 ./src/formats/gaussformat.cpp:450:29: note: ‘E0’ was declared here 2023-09-12T11:05:16,018 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:05:16,019 | ^~ 2023-09-12T11:05:16,019 ./src/formats/gaussformat.cpp:1164:25: warning: ‘Gcorr’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:16,020 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:05:16,021 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,022 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:05:16,023 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,024 ./src/formats/gaussformat.cpp:450:23: note: ‘Gcorr’ was declared here 2023-09-12T11:05:16,024 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:05:16,025 | ^~~~~ 2023-09-12T11:05:16,025 ./src/formats/gaussformat.cpp:1164:25: warning: ‘Hcorr’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:16,026 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:05:16,027 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,027 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:05:16,028 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,029 ./src/formats/gaussformat.cpp:450:17: note: ‘Hcorr’ was declared here 2023-09-12T11:05:16,029 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:05:16,030 | ^~~~~ 2023-09-12T11:05:16,030 ./src/formats/gaussformat.cpp:1164:25: warning: ‘ezpe’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:16,031 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:05:16,032 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,032 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:05:16,033 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,034 ./src/formats/gaussformat.cpp:450:12: note: ‘ezpe’ was declared here 2023-09-12T11:05:16,034 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:05:16,035 | ^~~~ 2023-09-12T11:05:16,128 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,129 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:609:42: 2023-09-12T11:05:16,129 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,130 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:16,131 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:16,132 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,132 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:610:42: 2023-09-12T11:05:16,133 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,134 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:16,134 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:16,135 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,136 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:611:42: 2023-09-12T11:05:16,136 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,137 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:16,138 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:16,147 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,148 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:05:16,149 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:841:34: 2023-09-12T11:05:16,149 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,150 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:16,150 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,151 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,151 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:05:16,152 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:847:34: 2023-09-12T11:05:16,152 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,153 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:16,154 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,154 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:05:16,155 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:05:16,156 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:866:31: 2023-09-12T11:05:16,157 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,157 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:16,158 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,159 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:05:16,159 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:05:16,160 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:868:31: 2023-09-12T11:05:16,161 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,162 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:16,162 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,163 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:05:16,164 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:05:16,164 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:870:31: 2023-09-12T11:05:16,165 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,165 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:16,166 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,167 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,167 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:05:16,168 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:904:32: 2023-09-12T11:05:16,168 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,169 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:16,170 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,170 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,171 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:05:16,172 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:964:33: 2023-09-12T11:05:16,173 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,173 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:16,174 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,178 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:16,178 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:1187:39: 2023-09-12T11:05:16,179 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:05:16,180 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:16,180 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:22,524 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gaussformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:22,525 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/gaussformat.o /tmp/ccOoMhPS.s 2023-09-12T11:05:22,532 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:23,719 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:05:23,720 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:05:23,720 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gaussformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/gaussformat.' 2023-09-12T11:05:23,724 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/gausszmatformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/gausszmatformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:05:23,729 Using built-in specs. 2023-09-12T11:05:23,729 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:23,730 Target: arm-linux-gnueabihf 2023-09-12T11:05:23,731 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:05:23,731 Thread model: posix 2023-09-12T11:05:23,732 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:23,732 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:23,733 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausszmatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:23,733 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gausszmatformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase gausszmatformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc71Xfli.s 2023-09-12T11:05:23,743 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:23,743 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:23,745 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:23,745 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:23,745 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:23,746 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:23,746 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:23,747 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:23,747 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:23,748 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:23,748 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:23,749 #include "..." search starts here: 2023-09-12T11:05:23,749 #include <...> search starts here: 2023-09-12T11:05:23,750 /usr/include/eigen3 2023-09-12T11:05:23,750 include 2023-09-12T11:05:23,751 /usr/include/python3.11 2023-09-12T11:05:23,751 /usr/include/c++/12 2023-09-12T11:05:23,752 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:23,753 /usr/include/c++/12/backward 2023-09-12T11:05:23,754 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:23,754 /usr/local/include 2023-09-12T11:05:23,755 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:23,755 /usr/include 2023-09-12T11:05:23,756 End of search list. 2023-09-12T11:05:23,757 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:23,757 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:23,758 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:23,759 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:23,762 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:25,347 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:25,347 from include/openbabel/mol.h:43, 2023-09-12T11:05:25,348 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:25,349 from ./src/formats/gausszmatformat.cpp:16: 2023-09-12T11:05:25,349 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:25,350 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:25,351 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:25,351 | ^ 2023-09-12T11:05:25,352 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:25,353 37 | # define UNUSED(x) x 2023-09-12T11:05:25,354 | ^ 2023-09-12T11:05:26,119 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:26,120 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:26,120 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:26,121 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:26,121 | ^ 2023-09-12T11:05:26,122 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:26,122 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:26,123 | ^~~~~~~~ 2023-09-12T11:05:26,125 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:26,125 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:26,126 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:26,126 | ^ 2023-09-12T11:05:26,127 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:26,128 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:26,128 | ^~~~~~~~ 2023-09-12T11:05:26,144 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:26,145 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:26,146 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:26,146 | ^ 2023-09-12T11:05:26,147 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:26,148 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:26,149 | ^~~~~~~~ 2023-09-12T11:05:26,151 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:26,152 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:26,153 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:26,153 | ^ 2023-09-12T11:05:26,154 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:26,155 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:26,155 | ^~~~~~~~ 2023-09-12T11:05:26,324 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:26,325 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:26,326 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:26,326 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:26,327 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:26,327 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:26,328 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:26,329 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:26,329 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:26,330 from include/openbabel/mol.h:35: 2023-09-12T11:05:26,330 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:26,331 131 | struct binary_function 2023-09-12T11:05:26,331 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:30,103 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:05:30,104 from include/openbabel/mol.h:37: 2023-09-12T11:05:30,110 /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:05:30,110 /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:05:30,111 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:05:30,112 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:31,770 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausszmatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:31,771 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/gausszmatformat.o /tmp/cc71Xfli.s 2023-09-12T11:05:31,776 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:32,155 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:05:32,155 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:05:32,156 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausszmatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/gausszmatformat.' 2023-09-12T11:05:32,158 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/genbankformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/genbankformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:05:32,162 Using built-in specs. 2023-09-12T11:05:32,163 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:32,163 Target: arm-linux-gnueabihf 2023-09-12T11:05:32,164 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:05:32,164 Thread model: posix 2023-09-12T11:05:32,165 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:32,165 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:32,166 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/genbankformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:32,166 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/genbankformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase genbankformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccAUdda2.s 2023-09-12T11:05:32,175 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:32,175 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:32,177 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:32,177 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:32,178 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:32,178 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:32,179 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:32,180 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:32,180 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:32,181 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:32,181 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:32,182 #include "..." search starts here: 2023-09-12T11:05:32,182 #include <...> search starts here: 2023-09-12T11:05:32,182 /usr/include/eigen3 2023-09-12T11:05:32,183 include 2023-09-12T11:05:32,183 /usr/include/python3.11 2023-09-12T11:05:32,184 /usr/include/c++/12 2023-09-12T11:05:32,184 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:32,185 /usr/include/c++/12/backward 2023-09-12T11:05:32,185 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:32,186 /usr/local/include 2023-09-12T11:05:32,186 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:32,187 /usr/include 2023-09-12T11:05:32,187 End of search list. 2023-09-12T11:05:32,188 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:32,188 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:32,189 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:32,190 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:32,193 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:33,766 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:33,767 from include/openbabel/mol.h:43, 2023-09-12T11:05:33,767 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:33,768 from ./src/formats/genbankformat.cpp:19: 2023-09-12T11:05:33,769 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:33,769 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:33,770 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:33,771 | ^ 2023-09-12T11:05:33,771 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:33,772 37 | # define UNUSED(x) x 2023-09-12T11:05:33,773 | ^ 2023-09-12T11:05:34,536 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:34,536 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:34,537 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:34,538 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:34,538 | ^ 2023-09-12T11:05:34,539 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:34,540 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:34,540 | ^~~~~~~~ 2023-09-12T11:05:34,541 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:34,542 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:34,543 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:34,544 | ^ 2023-09-12T11:05:34,544 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:34,545 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:34,545 | ^~~~~~~~ 2023-09-12T11:05:34,560 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:34,560 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:34,561 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:34,562 | ^ 2023-09-12T11:05:34,562 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:34,563 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:34,563 | ^~~~~~~~ 2023-09-12T11:05:34,566 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:34,567 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:34,567 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:34,568 | ^ 2023-09-12T11:05:34,569 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:34,569 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:34,570 | ^~~~~~~~ 2023-09-12T11:05:34,739 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:34,740 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:34,740 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:34,741 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:34,742 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:34,742 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:34,743 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:34,744 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:34,745 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:34,745 from include/openbabel/mol.h:35: 2023-09-12T11:05:34,746 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:34,746 131 | struct binary_function 2023-09-12T11:05:34,747 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:37,228 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/genbankformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:37,229 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/genbankformat.o /tmp/ccAUdda2.s 2023-09-12T11:05:37,233 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:37,383 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:05:37,384 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:05:37,384 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/genbankformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/genbankformat.' 2023-09-12T11:05:37,386 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/ghemicalformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/ghemicalformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:05:37,390 Using built-in specs. 2023-09-12T11:05:37,391 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:37,392 Target: arm-linux-gnueabihf 2023-09-12T11:05:37,392 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:05:37,393 Thread model: posix 2023-09-12T11:05:37,394 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:37,394 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:37,395 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/ghemicalformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:37,396 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/ghemicalformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase ghemicalformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccxDe1Sf.s 2023-09-12T11:05:37,403 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:37,404 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:37,405 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:37,406 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:37,406 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:37,406 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:37,407 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:37,407 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:37,408 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:37,408 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:37,409 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:37,410 #include "..." search starts here: 2023-09-12T11:05:37,410 #include <...> search starts here: 2023-09-12T11:05:37,411 /usr/include/eigen3 2023-09-12T11:05:37,411 include 2023-09-12T11:05:37,412 /usr/include/python3.11 2023-09-12T11:05:37,412 /usr/include/c++/12 2023-09-12T11:05:37,413 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:37,413 /usr/include/c++/12/backward 2023-09-12T11:05:37,414 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:37,415 /usr/local/include 2023-09-12T11:05:37,415 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:37,416 /usr/include 2023-09-12T11:05:37,416 End of search list. 2023-09-12T11:05:37,417 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:37,418 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:37,419 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:37,419 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:37,422 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:38,994 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:38,995 from include/openbabel/mol.h:43, 2023-09-12T11:05:38,996 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:38,996 from ./src/formats/ghemicalformat.cpp:17: 2023-09-12T11:05:38,997 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:38,998 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:38,998 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:38,999 | ^ 2023-09-12T11:05:39,000 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:39,000 37 | # define UNUSED(x) x 2023-09-12T11:05:39,001 | ^ 2023-09-12T11:05:39,764 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:39,765 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:39,766 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:39,766 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:39,767 | ^ 2023-09-12T11:05:39,768 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:39,768 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:39,769 | ^~~~~~~~ 2023-09-12T11:05:39,769 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:39,770 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:39,771 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:39,771 | ^ 2023-09-12T11:05:39,772 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:39,773 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:39,773 | ^~~~~~~~ 2023-09-12T11:05:39,789 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:39,790 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:39,791 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:39,792 | ^ 2023-09-12T11:05:39,792 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:39,793 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:39,794 | ^~~~~~~~ 2023-09-12T11:05:39,795 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:39,796 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:39,797 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:39,797 | ^ 2023-09-12T11:05:39,798 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:39,799 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:39,799 | ^~~~~~~~ 2023-09-12T11:05:39,968 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:39,969 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:39,970 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:39,971 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:39,971 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:39,972 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:39,972 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:39,973 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:39,974 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:39,974 from include/openbabel/mol.h:35: 2023-09-12T11:05:39,975 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:39,975 131 | struct binary_function 2023-09-12T11:05:39,976 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:43,253 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/ghemicalformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:43,254 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/ghemicalformat.o /tmp/ccxDe1Sf.s 2023-09-12T11:05:43,259 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:43,462 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:05:43,463 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:05:43,464 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/ghemicalformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/ghemicalformat.' 2023-09-12T11:05:43,464 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/groformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/groformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:05:43,469 Using built-in specs. 2023-09-12T11:05:43,469 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:43,470 Target: arm-linux-gnueabihf 2023-09-12T11:05:43,471 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:05:43,471 Thread model: posix 2023-09-12T11:05:43,472 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:43,472 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:43,473 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/groformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:43,474 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/groformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase groformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccO0xhaI.s 2023-09-12T11:05:43,482 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:43,483 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:43,484 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:43,484 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:43,485 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:43,486 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:43,486 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:43,487 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:43,488 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:43,488 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:43,489 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:43,489 #include "..." search starts here: 2023-09-12T11:05:43,490 #include <...> search starts here: 2023-09-12T11:05:43,490 /usr/include/eigen3 2023-09-12T11:05:43,491 include 2023-09-12T11:05:43,492 /usr/include/python3.11 2023-09-12T11:05:43,492 /usr/include/c++/12 2023-09-12T11:05:43,493 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:43,493 /usr/include/c++/12/backward 2023-09-12T11:05:43,494 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:43,495 /usr/local/include 2023-09-12T11:05:43,495 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:43,496 /usr/include 2023-09-12T11:05:43,497 End of search list. 2023-09-12T11:05:43,497 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:43,498 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:43,500 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:43,500 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:43,501 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:45,077 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:45,078 from include/openbabel/mol.h:43, 2023-09-12T11:05:45,078 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:45,079 from ./src/formats/groformat.cpp:16: 2023-09-12T11:05:45,079 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:45,080 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:45,080 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:45,081 | ^ 2023-09-12T11:05:45,081 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:45,082 37 | # define UNUSED(x) x 2023-09-12T11:05:45,082 | ^ 2023-09-12T11:05:45,846 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:45,847 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:45,848 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:45,848 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:45,849 | ^ 2023-09-12T11:05:45,850 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:45,850 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:45,851 | ^~~~~~~~ 2023-09-12T11:05:45,852 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:45,853 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:45,853 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:45,854 | ^ 2023-09-12T11:05:45,855 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:45,855 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:45,856 | ^~~~~~~~ 2023-09-12T11:05:45,870 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:45,871 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:45,872 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:45,873 | ^ 2023-09-12T11:05:45,873 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:45,874 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:45,875 | ^~~~~~~~ 2023-09-12T11:05:45,877 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:45,878 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:45,878 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:45,879 | ^ 2023-09-12T11:05:45,880 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:45,880 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:45,881 | ^~~~~~~~ 2023-09-12T11:05:46,050 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:46,050 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:46,051 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:46,052 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:46,052 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:46,053 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:46,053 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:46,054 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:46,055 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:46,055 from include/openbabel/mol.h:35: 2023-09-12T11:05:46,056 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:46,057 131 | struct binary_function 2023-09-12T11:05:46,058 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:50,081 ./src/formats/groformat.cpp: In member function ‘virtual bool OpenBabel::GROFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:50,082 ./src/formats/groformat.cpp:273:19: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:50,082 273 | res->AddAtom(atom); 2023-09-12T11:05:50,083 | ~~~~~~~~~~~~^~~~~~ 2023-09-12T11:05:50,084 ./src/formats/groformat.cpp:163:14: note: ‘res’ was declared here 2023-09-12T11:05:50,085 163 | OBResidue* res; 2023-09-12T11:05:50,086 | ^~~ 2023-09-12T11:05:52,486 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/groformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:52,487 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/groformat.o /tmp/ccO0xhaI.s 2023-09-12T11:05:52,499 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:52,926 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:05:52,927 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:05:52,929 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/groformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/groformat.' 2023-09-12T11:05:52,930 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/gromos96format.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/gromos96format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:05:52,933 Using built-in specs. 2023-09-12T11:05:52,934 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:52,935 Target: arm-linux-gnueabihf 2023-09-12T11:05:52,935 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:05:52,936 Thread model: posix 2023-09-12T11:05:52,937 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:52,937 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:52,938 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gromos96format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:52,939 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gromos96format.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase gromos96format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc0IdN3L.s 2023-09-12T11:05:52,947 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:52,948 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:52,949 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:52,950 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:52,950 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:52,951 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:52,951 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:52,952 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:52,952 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:52,952 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:52,953 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:52,953 #include "..." search starts here: 2023-09-12T11:05:52,954 #include <...> search starts here: 2023-09-12T11:05:52,954 /usr/include/eigen3 2023-09-12T11:05:52,955 include 2023-09-12T11:05:52,955 /usr/include/python3.11 2023-09-12T11:05:52,956 /usr/include/c++/12 2023-09-12T11:05:52,956 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:52,957 /usr/include/c++/12/backward 2023-09-12T11:05:52,957 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:52,958 /usr/local/include 2023-09-12T11:05:52,958 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:52,959 /usr/include 2023-09-12T11:05:52,959 End of search list. 2023-09-12T11:05:52,960 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:52,960 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:52,961 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:52,962 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:52,969 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:54,540 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:54,541 from include/openbabel/mol.h:43, 2023-09-12T11:05:54,542 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:54,542 from ./src/formats/gromos96format.cpp:54: 2023-09-12T11:05:54,543 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:54,544 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:54,545 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:54,545 | ^ 2023-09-12T11:05:54,546 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:54,547 37 | # define UNUSED(x) x 2023-09-12T11:05:54,547 | ^ 2023-09-12T11:05:55,311 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:55,311 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:55,312 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:55,313 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:55,313 | ^ 2023-09-12T11:05:55,314 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:55,315 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:55,316 | ^~~~~~~~ 2023-09-12T11:05:55,316 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:55,317 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:55,317 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:55,318 | ^ 2023-09-12T11:05:55,318 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:55,319 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:55,319 | ^~~~~~~~ 2023-09-12T11:05:55,335 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:55,336 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:55,337 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:55,337 | ^ 2023-09-12T11:05:55,338 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:55,338 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:55,339 | ^~~~~~~~ 2023-09-12T11:05:55,342 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:55,343 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:55,343 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:55,344 | ^ 2023-09-12T11:05:55,345 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:55,346 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:55,346 | ^~~~~~~~ 2023-09-12T11:05:55,516 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:55,517 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:55,518 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:55,518 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:55,519 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:55,519 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:55,520 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:55,521 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:55,522 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:55,522 from include/openbabel/mol.h:35: 2023-09-12T11:05:55,523 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:55,524 131 | struct binary_function 2023-09-12T11:05:55,524 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:57,333 ./src/formats/gromos96format.cpp: In member function ‘virtual bool OpenBabel::GROMOS96Format::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:57,334 ./src/formats/gromos96format.cpp:140:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2023-09-12T11:05:57,334 140 | strncpy(type_name,etab.GetSymbol(atom->GetAtomicNum()), 16); 2023-09-12T11:05:57,335 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:57,336 ./src/formats/gromos96format.cpp:132:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2023-09-12T11:05:57,337 132 | strncpy(res_name,(char*)res->GetName().c_str(), 16); 2023-09-12T11:05:57,337 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:57,338 ./src/formats/gromos96format.cpp:134:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2023-09-12T11:05:57,339 134 | strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16); 2023-09-12T11:05:57,339 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:57,999 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gromos96format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:57,999 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/gromos96format.o /tmp/cc0IdN3L.s 2023-09-12T11:05:58,004 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:58,147 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:05:58,148 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:05:58,149 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gromos96format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/gromos96format.' 2023-09-12T11:05:58,150 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/gulpformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/gulpformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:05:58,154 Using built-in specs. 2023-09-12T11:05:58,154 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:58,155 Target: arm-linux-gnueabihf 2023-09-12T11:05:58,156 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:05:58,156 Thread model: posix 2023-09-12T11:05:58,157 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:58,157 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:58,158 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gulpformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:05:58,158 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gulpformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase gulpformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccE7QC7Y.s 2023-09-12T11:05:58,167 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:58,168 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:58,169 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:58,170 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:58,170 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:58,170 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:58,171 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:58,171 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:58,172 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:58,173 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:58,173 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:58,174 #include "..." search starts here: 2023-09-12T11:05:58,174 #include <...> search starts here: 2023-09-12T11:05:58,175 /usr/include/eigen3 2023-09-12T11:05:58,176 include 2023-09-12T11:05:58,176 /usr/include/python3.11 2023-09-12T11:05:58,177 /usr/include/c++/12 2023-09-12T11:05:58,178 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:58,178 /usr/include/c++/12/backward 2023-09-12T11:05:58,179 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:58,180 /usr/local/include 2023-09-12T11:05:58,180 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:58,181 /usr/include 2023-09-12T11:05:58,181 End of search list. 2023-09-12T11:05:58,181 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:58,182 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:58,183 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:58,183 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:58,189 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:59,751 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:59,752 from include/openbabel/mol.h:43, 2023-09-12T11:05:59,752 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:59,753 from ./src/formats/gulpformat.cpp:16: 2023-09-12T11:05:59,754 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:59,754 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:59,755 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:59,755 | ^ 2023-09-12T11:05:59,756 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:59,756 37 | # define UNUSED(x) x 2023-09-12T11:05:59,757 | ^ 2023-09-12T11:06:00,520 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:00,521 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:00,521 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:00,522 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:00,523 | ^ 2023-09-12T11:06:00,524 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:00,524 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:00,525 | ^~~~~~~~ 2023-09-12T11:06:00,526 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:00,526 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:00,527 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:00,528 | ^ 2023-09-12T11:06:00,528 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:00,529 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:00,530 | ^~~~~~~~ 2023-09-12T11:06:00,544 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:00,545 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:00,546 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:00,547 | ^ 2023-09-12T11:06:00,548 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:00,548 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:00,549 | ^~~~~~~~ 2023-09-12T11:06:00,551 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:00,551 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:00,552 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:00,553 | ^ 2023-09-12T11:06:00,553 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:00,554 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:00,554 | ^~~~~~~~ 2023-09-12T11:06:00,724 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:00,724 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:00,725 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:00,725 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:00,726 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:00,727 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:00,728 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:00,728 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:00,729 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:00,730 from include/openbabel/mol.h:35: 2023-09-12T11:06:00,730 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:00,731 131 | struct binary_function 2023-09-12T11:06:00,732 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:00,923 ./src/formats/gulpformat.cpp: In member function ‘virtual int OpenBabel::GULPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:06:00,923 ./src/formats/gulpformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:06:00,924 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:06:00,925 | ~~~~^ 2023-09-12T11:06:00,925 ./src/formats/gulpformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:06:00,926 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:06:00,927 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:06:03,697 ./src/formats/gulpformat.cpp: In member function ‘virtual bool OpenBabel::GULPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:03,698 ./src/formats/gulpformat.cpp:359:15: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:03,698 359 | snprintf(tag, BUFF_SIZE, "%f", pv_eV); 2023-09-12T11:06:03,699 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:03,700 ./src/formats/gulpformat.cpp:88:25: note: ‘pv_eV’ was declared here 2023-09-12T11:06:03,701 88 | double enthalpy_eV, pv_eV; 2023-09-12T11:06:03,702 | ^~~~~ 2023-09-12T11:06:03,703 ./src/formats/gulpformat.cpp:357:15: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:03,704 357 | snprintf(tag, BUFF_SIZE, "%f", enthalpy_eV); 2023-09-12T11:06:03,705 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:03,706 ./src/formats/gulpformat.cpp:88:12: note: ‘enthalpy_eV’ was declared here 2023-09-12T11:06:03,706 88 | double enthalpy_eV, pv_eV; 2023-09-12T11:06:03,707 | ^~~~~~~~~~~ 2023-09-12T11:06:05,131 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gulpformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:05,132 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/gulpformat.o /tmp/ccE7QC7Y.s 2023-09-12T11:06:05,137 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:05,410 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:06:05,411 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:06:05,411 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/gulpformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/gulpformat.' 2023-09-12T11:06:05,413 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/hinformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/hinformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:05,417 Using built-in specs. 2023-09-12T11:06:05,418 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:05,418 Target: arm-linux-gnueabihf 2023-09-12T11:06:05,419 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:06:05,420 Thread model: posix 2023-09-12T11:06:05,420 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:05,421 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:05,421 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/hinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:05,422 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/hinformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase hinformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cclczY35.s 2023-09-12T11:06:05,430 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:05,431 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:05,432 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:05,432 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:05,433 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:05,433 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:05,434 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:05,435 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:05,435 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:05,436 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:05,437 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:05,437 #include "..." search starts here: 2023-09-12T11:06:05,438 #include <...> search starts here: 2023-09-12T11:06:05,438 /usr/include/eigen3 2023-09-12T11:06:05,439 include 2023-09-12T11:06:05,440 /usr/include/python3.11 2023-09-12T11:06:05,440 /usr/include/c++/12 2023-09-12T11:06:05,441 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:05,441 /usr/include/c++/12/backward 2023-09-12T11:06:05,442 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:05,442 /usr/local/include 2023-09-12T11:06:05,443 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:05,444 /usr/include 2023-09-12T11:06:05,444 End of search list. 2023-09-12T11:06:05,445 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:05,445 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:05,446 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:05,447 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:05,448 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:07,019 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:07,020 from include/openbabel/mol.h:43, 2023-09-12T11:06:07,021 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:07,021 from ./src/formats/hinformat.cpp:17: 2023-09-12T11:06:07,022 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:07,022 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:07,023 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:07,023 | ^ 2023-09-12T11:06:07,024 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:07,024 37 | # define UNUSED(x) x 2023-09-12T11:06:07,025 | ^ 2023-09-12T11:06:07,790 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:07,791 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,792 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,792 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:07,793 | ^ 2023-09-12T11:06:07,793 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:07,794 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:07,795 | ^~~~~~~~ 2023-09-12T11:06:07,796 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,796 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,797 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:07,798 | ^ 2023-09-12T11:06:07,799 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:07,799 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:07,800 | ^~~~~~~~ 2023-09-12T11:06:07,815 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,816 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,816 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:07,817 | ^ 2023-09-12T11:06:07,817 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:07,818 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:07,819 | ^~~~~~~~ 2023-09-12T11:06:07,821 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,822 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,823 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:07,824 | ^ 2023-09-12T11:06:07,824 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:07,825 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:07,825 | ^~~~~~~~ 2023-09-12T11:06:07,995 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:07,995 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:07,996 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:07,996 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:07,997 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:07,997 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:07,998 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:07,998 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:07,999 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:08,000 from include/openbabel/mol.h:35: 2023-09-12T11:06:08,000 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:08,001 131 | struct binary_function 2023-09-12T11:06:08,002 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:10,827 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/hinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:10,828 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/hinformat.o /tmp/cclczY35.s 2023-09-12T11:06:10,832 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:11,007 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:06:11,008 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:06:11,009 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/hinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/hinformat.' 2023-09-12T11:06:11,009 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/jaguarformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/jaguarformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:11,013 Using built-in specs. 2023-09-12T11:06:11,014 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:11,015 Target: arm-linux-gnueabihf 2023-09-12T11:06:11,015 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:06:11,016 Thread model: posix 2023-09-12T11:06:11,016 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:11,017 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:11,017 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/jaguarformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:11,018 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/jaguarformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase jaguarformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccoGKmej.s 2023-09-12T11:06:11,026 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:11,027 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:11,028 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:11,029 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:11,029 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:11,030 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:11,030 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:11,031 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:11,032 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:11,032 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:11,033 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:11,033 #include "..." search starts here: 2023-09-12T11:06:11,034 #include <...> search starts here: 2023-09-12T11:06:11,035 /usr/include/eigen3 2023-09-12T11:06:11,035 include 2023-09-12T11:06:11,036 /usr/include/python3.11 2023-09-12T11:06:11,036 /usr/include/c++/12 2023-09-12T11:06:11,037 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:11,037 /usr/include/c++/12/backward 2023-09-12T11:06:11,037 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:11,038 /usr/local/include 2023-09-12T11:06:11,038 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:11,039 /usr/include 2023-09-12T11:06:11,039 End of search list. 2023-09-12T11:06:11,039 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:11,040 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:11,041 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:11,041 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:11,046 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:12,625 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:12,625 from include/openbabel/mol.h:43, 2023-09-12T11:06:12,626 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:12,627 from ./src/formats/jaguarformat.cpp:17: 2023-09-12T11:06:12,627 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:12,628 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:12,628 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:12,629 | ^ 2023-09-12T11:06:12,630 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:12,630 37 | # define UNUSED(x) x 2023-09-12T11:06:12,631 | ^ 2023-09-12T11:06:13,405 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:13,406 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:13,407 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:13,407 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:13,408 | ^ 2023-09-12T11:06:13,409 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:13,410 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:13,410 | ^~~~~~~~ 2023-09-12T11:06:13,411 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:13,412 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:13,412 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:13,413 | ^ 2023-09-12T11:06:13,414 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:13,415 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:13,415 | ^~~~~~~~ 2023-09-12T11:06:13,430 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:13,431 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:13,432 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:13,432 | ^ 2023-09-12T11:06:13,433 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:13,434 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:13,434 | ^~~~~~~~ 2023-09-12T11:06:13,437 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:13,438 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:13,438 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:13,439 | ^ 2023-09-12T11:06:13,440 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:13,440 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:13,441 | ^~~~~~~~ 2023-09-12T11:06:13,610 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:13,611 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:13,612 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:13,613 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:13,613 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:13,614 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:13,615 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:13,616 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:13,616 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:13,617 from include/openbabel/mol.h:35: 2023-09-12T11:06:13,618 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:13,618 131 | struct binary_function 2023-09-12T11:06:13,619 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:17,108 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/jaguarformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:17,109 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/jaguarformat.o /tmp/ccoGKmej.s 2023-09-12T11:06:17,114 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:17,339 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:06:17,340 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:06:17,340 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/jaguarformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/jaguarformat.' 2023-09-12T11:06:17,342 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/lmpdatformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/lmpdatformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:17,345 Using built-in specs. 2023-09-12T11:06:17,346 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:17,347 Target: arm-linux-gnueabihf 2023-09-12T11:06:17,347 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:06:17,348 Thread model: posix 2023-09-12T11:06:17,348 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:17,349 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:17,350 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/lmpdatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:17,350 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/lmpdatformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase lmpdatformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccrdTvqJ.s 2023-09-12T11:06:17,359 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:17,360 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:17,361 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:17,361 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:17,361 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:17,362 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:17,362 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:17,362 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:17,363 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:17,364 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:17,364 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:17,364 #include "..." search starts here: 2023-09-12T11:06:17,365 #include <...> search starts here: 2023-09-12T11:06:17,365 /usr/include/eigen3 2023-09-12T11:06:17,366 include 2023-09-12T11:06:17,366 /usr/include/python3.11 2023-09-12T11:06:17,366 /usr/include/c++/12 2023-09-12T11:06:17,367 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:17,367 /usr/include/c++/12/backward 2023-09-12T11:06:17,368 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:17,368 /usr/local/include 2023-09-12T11:06:17,369 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:17,369 /usr/include 2023-09-12T11:06:17,370 End of search list. 2023-09-12T11:06:17,370 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:17,371 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:17,372 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:17,373 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:17,378 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:20,509 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:20,510 from include/openbabel/mol.h:43, 2023-09-12T11:06:20,511 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:20,512 from ./src/formats/lmpdatformat.cpp:15: 2023-09-12T11:06:20,512 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:20,513 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:20,514 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:20,515 | ^ 2023-09-12T11:06:20,516 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:20,517 37 | # define UNUSED(x) x 2023-09-12T11:06:20,518 | ^ 2023-09-12T11:06:21,834 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:21,834 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:21,835 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:21,836 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:21,837 | ^ 2023-09-12T11:06:21,838 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:21,839 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:21,839 | ^~~~~~~~ 2023-09-12T11:06:21,840 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:21,840 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:21,841 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:21,842 | ^ 2023-09-12T11:06:21,842 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:21,843 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:21,844 | ^~~~~~~~ 2023-09-12T11:06:21,859 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:21,860 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:21,861 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:21,861 | ^ 2023-09-12T11:06:21,862 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:21,863 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:21,864 | ^~~~~~~~ 2023-09-12T11:06:21,866 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:21,867 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:21,868 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:21,869 | ^ 2023-09-12T11:06:21,870 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:21,870 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:21,871 | ^~~~~~~~ 2023-09-12T11:06:22,065 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:22,065 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:22,066 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:22,067 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:22,068 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:22,069 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:22,070 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:22,071 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:22,072 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:22,072 from include/openbabel/mol.h:35: 2023-09-12T11:06:22,073 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:22,074 131 | struct binary_function 2023-09-12T11:06:22,074 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:22,390 ./src/formats/lmpdatformat.cpp: In member function ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:22,391 ./src/formats/lmpdatformat.cpp:271:20: warning: unused variable ‘length’ [-Wunused-variable] 2023-09-12T11:06:22,391 271 | double length=cmax-cmin; 2023-09-12T11:06:22,392 | ^~~~~~ 2023-09-12T11:06:22,427 ./src/formats/lmpdatformat.cpp:361:25: warning: unused variable ‘atomid’ [-Wunused-variable] 2023-09-12T11:06:22,427 361 | int atomid=5; 2023-09-12T11:06:22,428 | ^~~~~~ 2023-09-12T11:06:22,428 ./src/formats/lmpdatformat.cpp:362:28: warning: unused variable ‘charge’ [-Wunused-variable] 2023-09-12T11:06:22,429 362 | double charge=0.5; 2023-09-12T11:06:22,430 | ^~~~~~ 2023-09-12T11:06:25,764 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:06:25,765 from include/openbabel/mol.h:37: 2023-09-12T11:06:25,766 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:06:25,766 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:25,767 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:06:25,768 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:25,877 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:06:25,878 /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:06:25,879 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:25,879 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:06:25,880 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:25,880 512 | std::tuple(__k), 2023-09-12T11:06:25,881 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:25,882 513 | std::tuple<>()); 2023-09-12T11:06:25,883 | ~~~~~~~~~~~~~~~ 2023-09-12T11:06:27,239 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:06:27,241 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:98:21: 2023-09-12T11:06:27,248 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:27,256 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:06:27,260 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:27,272 512 | std::tuple(__k), 2023-09-12T11:06:27,280 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:27,288 513 | std::tuple<>()); 2023-09-12T11:06:27,292 | ~~~~~~~~~~~~~~~ 2023-09-12T11:06:27,292 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:06:27,293 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:368:28: 2023-09-12T11:06:27,294 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:27,295 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:06:27,297 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:27,297 512 | std::tuple(__k), 2023-09-12T11:06:27,298 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:27,299 513 | std::tuple<>()); 2023-09-12T11:06:27,299 | ~~~~~~~~~~~~~~~ 2023-09-12T11:06:30,006 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/lmpdatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:30,006 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/lmpdatformat.o /tmp/ccrdTvqJ.s 2023-09-12T11:06:30,013 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:30,546 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:06:30,546 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:06:30,547 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/lmpdatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/lmpdatformat.' 2023-09-12T11:06:30,549 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/lpmdformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/lpmdformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:30,554 Using built-in specs. 2023-09-12T11:06:30,555 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:30,555 Target: arm-linux-gnueabihf 2023-09-12T11:06:30,556 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:06:30,556 Thread model: posix 2023-09-12T11:06:30,557 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:30,557 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:30,558 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/lpmdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:30,558 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/lpmdformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase lpmdformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccN5kyWd.s 2023-09-12T11:06:30,568 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:30,568 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:30,569 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:30,570 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:30,570 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:30,570 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:30,571 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:30,571 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:30,572 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:30,572 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:30,573 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:30,573 #include "..." search starts here: 2023-09-12T11:06:30,574 #include <...> search starts here: 2023-09-12T11:06:30,574 /usr/include/eigen3 2023-09-12T11:06:30,575 include 2023-09-12T11:06:30,575 /usr/include/python3.11 2023-09-12T11:06:30,576 /usr/include/c++/12 2023-09-12T11:06:30,576 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:30,577 /usr/include/c++/12/backward 2023-09-12T11:06:30,577 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:30,578 /usr/local/include 2023-09-12T11:06:30,578 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:30,579 /usr/include 2023-09-12T11:06:30,579 End of search list. 2023-09-12T11:06:30,580 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:30,580 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:30,581 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:30,582 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:30,585 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:32,169 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:32,170 from include/openbabel/mol.h:43, 2023-09-12T11:06:32,170 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:32,171 from ./src/formats/lpmdformat.cpp:15: 2023-09-12T11:06:32,172 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:32,173 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:32,173 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:32,174 | ^ 2023-09-12T11:06:32,175 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:32,175 37 | # define UNUSED(x) x 2023-09-12T11:06:32,176 | ^ 2023-09-12T11:06:32,941 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:32,942 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:32,943 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:32,943 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:32,944 | ^ 2023-09-12T11:06:32,944 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:32,945 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:32,945 | ^~~~~~~~ 2023-09-12T11:06:32,946 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:32,947 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:32,948 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:32,948 | ^ 2023-09-12T11:06:32,949 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:32,949 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:32,950 | ^~~~~~~~ 2023-09-12T11:06:32,966 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:32,966 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:32,967 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:32,968 | ^ 2023-09-12T11:06:32,969 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:32,969 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:32,970 | ^~~~~~~~ 2023-09-12T11:06:32,972 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:32,973 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:32,974 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:32,975 | ^ 2023-09-12T11:06:32,975 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:32,976 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:32,977 | ^~~~~~~~ 2023-09-12T11:06:33,146 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:33,146 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:33,147 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:33,148 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:33,149 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:33,150 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:33,150 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:33,151 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:33,151 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:33,152 from include/openbabel/mol.h:35: 2023-09-12T11:06:33,152 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:33,153 131 | struct binary_function 2023-09-12T11:06:33,153 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:33,363 ./src/formats/lpmdformat.cpp: In member function ‘virtual int OpenBabel::LpmdFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:06:33,364 ./src/formats/lpmdformat.cpp:56:31: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:06:33,364 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:06:33,365 | ~~~~^ 2023-09-12T11:06:33,365 ./src/formats/lpmdformat.cpp:56:48: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:06:33,366 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:06:33,366 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:06:33,371 ./src/formats/lpmdformat.cpp: In member function ‘bool OpenBabel::LpmdFormat::ReadHeader(std::istream&, OpenBabel::OBMol&)’: 2023-09-12T11:06:33,371 ./src/formats/lpmdformat.cpp:91:56: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T11:06:33,372 91 | bool LpmdFormat::ReadHeader( std::istream &ifs, OBMol &mol ) 2023-09-12T11:06:33,372 | ~~~~~~~^~~ 2023-09-12T11:06:33,378 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:33,378 ./src/formats/lpmdformat.cpp:190:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:33,379 190 | if(int(headers.size()-1)!=tokens.size()) 2023-09-12T11:06:33,380 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T11:06:33,383 ./src/formats/lpmdformat.cpp:204:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:33,384 204 | for(int i=1 ; i < headers.size() ; ++i) //the first element is HDR 2023-09-12T11:06:33,385 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T11:06:33,391 ./src/formats/lpmdformat.cpp:237:11: warning: unused variable ‘FX’ [-Wunused-variable] 2023-09-12T11:06:33,391 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2023-09-12T11:06:33,392 | ^~ 2023-09-12T11:06:33,393 ./src/formats/lpmdformat.cpp:237:32: warning: unused variable ‘FY’ [-Wunused-variable] 2023-09-12T11:06:33,393 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2023-09-12T11:06:33,394 | ^~ 2023-09-12T11:06:33,394 ./src/formats/lpmdformat.cpp:237:53: warning: unused variable ‘FZ’ [-Wunused-variable] 2023-09-12T11:06:33,395 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2023-09-12T11:06:33,396 | ^~ 2023-09-12T11:06:33,411 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:33,412 ./src/formats/lpmdformat.cpp:360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:06:33,413 360 | for(int i=0; i < mol.NumAtoms() ; ++i) 2023-09-12T11:06:33,414 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T11:06:33,415 ./src/formats/lpmdformat.cpp:376:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:06:33,415 376 | for(int i=0;i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:06:37,067 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:37,067 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:06:37,068 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,114 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:38,115 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:38,115 inlined from ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:239:19: 2023-09-12T11:06:38,116 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:38,117 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,117 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,118 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:38,119 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:38,120 inlined from ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:240:19: 2023-09-12T11:06:38,120 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:38,121 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,122 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:40,277 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:40,277 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:40,278 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:300:14: 2023-09-12T11:06:40,278 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:40,279 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:40,280 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:40,280 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:40,281 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:40,282 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:301:14: 2023-09-12T11:06:40,282 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:40,283 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:40,283 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:40,284 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:40,284 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:40,285 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:302:14: 2023-09-12T11:06:40,285 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:40,286 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:40,287 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:40,287 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:40,288 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:40,288 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:357:18: 2023-09-12T11:06:40,289 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:40,290 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:40,290 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:40,291 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:40,291 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:40,292 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:358:18: 2023-09-12T11:06:40,293 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:40,294 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:40,295 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:40,295 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:40,296 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:06:40,297 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:359:18: 2023-09-12T11:06:40,297 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:06:40,298 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:40,299 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:41,894 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/lpmdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:41,895 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/lpmdformat.o /tmp/ccN5kyWd.s 2023-09-12T11:06:41,899 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:42,539 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:06:42,540 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:06:42,540 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/lpmdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/lpmdformat.' 2023-09-12T11:06:42,543 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mdffformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mdffformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:42,547 Using built-in specs. 2023-09-12T11:06:42,548 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:42,549 Target: arm-linux-gnueabihf 2023-09-12T11:06:42,549 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:06:42,550 Thread model: posix 2023-09-12T11:06:42,550 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:42,551 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:42,551 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdffformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:42,552 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mdffformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mdffformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc6UnkVl.s 2023-09-12T11:06:42,560 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:42,561 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:42,562 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:42,562 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:42,563 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:42,564 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:42,564 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:42,565 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:42,565 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:42,566 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:42,566 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:42,567 #include "..." search starts here: 2023-09-12T11:06:42,568 #include <...> search starts here: 2023-09-12T11:06:42,568 /usr/include/eigen3 2023-09-12T11:06:42,569 include 2023-09-12T11:06:42,570 /usr/include/python3.11 2023-09-12T11:06:42,570 /usr/include/c++/12 2023-09-12T11:06:42,571 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:42,572 /usr/include/c++/12/backward 2023-09-12T11:06:42,573 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:42,574 /usr/local/include 2023-09-12T11:06:42,574 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:42,574 /usr/include 2023-09-12T11:06:42,575 End of search list. 2023-09-12T11:06:42,575 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:42,576 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:42,577 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:42,577 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:42,581 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:44,164 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:44,165 from include/openbabel/mol.h:43, 2023-09-12T11:06:44,165 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:44,166 from ./src/formats/mdffformat.cpp:17: 2023-09-12T11:06:44,167 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:44,167 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:44,168 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:44,168 | ^ 2023-09-12T11:06:44,169 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:44,169 37 | # define UNUSED(x) x 2023-09-12T11:06:44,170 | ^ 2023-09-12T11:06:44,942 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:44,943 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:44,943 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:44,944 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:44,945 | ^ 2023-09-12T11:06:44,946 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:44,947 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:44,947 | ^~~~~~~~ 2023-09-12T11:06:44,948 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:44,949 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:44,950 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:44,950 | ^ 2023-09-12T11:06:44,951 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:44,952 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:44,953 | ^~~~~~~~ 2023-09-12T11:06:44,967 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:44,968 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:44,969 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:44,970 | ^ 2023-09-12T11:06:44,971 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:44,971 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:44,972 | ^~~~~~~~ 2023-09-12T11:06:44,974 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:44,975 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:44,975 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:44,976 | ^ 2023-09-12T11:06:44,977 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:44,977 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:44,978 | ^~~~~~~~ 2023-09-12T11:06:45,148 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:45,148 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:45,149 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:45,150 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:45,150 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:45,151 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:45,152 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:45,153 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:45,154 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:45,154 from include/openbabel/mol.h:35: 2023-09-12T11:06:45,155 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:45,156 131 | struct binary_function 2023-09-12T11:06:45,157 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:45,470 ./src/formats/mdffformat.cpp: In member function ‘virtual int OpenBabel::MDFFFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:06:45,471 ./src/formats/mdffformat.cpp:71:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:06:45,471 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:06:45,472 | ~~~~^ 2023-09-12T11:06:45,473 ./src/formats/mdffformat.cpp:71:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:06:45,473 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:06:45,474 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:06:45,506 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:45,507 ./src/formats/mdffformat.cpp:241:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:45,507 241 | for(int i = 0; i < atom_t_prop.size(); i++) 2023-09-12T11:06:45,508 | ~~^~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:45,509 ./src/formats/mdffformat.cpp:262:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:06:45,510 262 | for(unsigned int j = 0; j < atom_t_prop[i].num_of_atoms; j++) 2023-09-12T11:06:45,511 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:45,519 ./src/formats/mdffformat.cpp: In member function ‘bool OpenBabel::aindx::operator<(const OpenBabel::aindx&) const’: 2023-09-12T11:06:45,520 ./src/formats/mdffformat.cpp:321:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:45,520 321 | for(int i = 0; i < vs.size(); i++) 2023-09-12T11:06:45,521 | ~~^~~~~~~~~~~ 2023-09-12T11:06:45,557 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:45,558 ./src/formats/mdffformat.cpp:380:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:45,558 380 | for(int i = 0; i < vs.size(); i++) 2023-09-12T11:06:45,559 | ~~^~~~~~~~~~~ 2023-09-12T11:06:45,639 ./src/formats/mdffformat.cpp:435:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, unsigned int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:45,640 435 | for (int i = 0; i < atypes_def.size(); i++) 2023-09-12T11:06:45,640 | ~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:45,641 ./src/formats/mdffformat.cpp:442:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, unsigned int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:45,642 442 | for (int i = 0; i < atypes_def.size(); i++) 2023-09-12T11:06:45,643 | ~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:45,684 ./src/formats/mdffformat.cpp:492:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, unsigned int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:06:45,685 492 | for(int j = 0; j < atypes_def.size(); j++) 2023-09-12T11:06:45,686 | ~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:52,472 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:06:52,472 from include/openbabel/mol.h:37: 2023-09-12T11:06:52,473 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:06:52,474 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:52,474 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:06:52,475 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,442 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:06:53,442 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:06:53,443 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:464:23: 2023-09-12T11:06:53,443 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:53,444 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:06:53,445 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,445 512 | std::tuple(__k), 2023-09-12T11:06:53,446 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,446 513 | std::tuple<>()); 2023-09-12T11:06:53,447 | ~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,448 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:06:53,449 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:466:26: 2023-09-12T11:06:53,449 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:53,450 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:06:53,451 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,452 512 | std::tuple(__k), 2023-09-12T11:06:53,452 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,453 513 | std::tuple<>()); 2023-09-12T11:06:53,453 | ~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,454 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:06:53,455 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:467:25: 2023-09-12T11:06:53,456 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:53,457 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:06:53,457 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,458 512 | std::tuple(__k), 2023-09-12T11:06:53,458 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,459 513 | std::tuple<>()); 2023-09-12T11:06:53,459 | ~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,460 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:06:53,460 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:499:53: 2023-09-12T11:06:53,461 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:06:53,461 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:06:53,462 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,463 512 | std::tuple(__k), 2023-09-12T11:06:53,464 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:53,464 513 | std::tuple<>()); 2023-09-12T11:06:53,465 | ~~~~~~~~~~~~~~~ 2023-09-12T11:06:55,498 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdffformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:55,498 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mdffformat.o /tmp/cc6UnkVl.s 2023-09-12T11:06:55,503 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:56,195 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:06:56,196 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:06:56,197 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdffformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdffformat.' 2023-09-12T11:06:56,200 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mdlformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mdlformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:56,203 Using built-in specs. 2023-09-12T11:06:56,204 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:56,205 Target: arm-linux-gnueabihf 2023-09-12T11:06:56,205 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:06:56,205 Thread model: posix 2023-09-12T11:06:56,206 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:56,207 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:56,207 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:06:56,208 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mdlformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mdlformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccuu4BYh.s 2023-09-12T11:06:56,216 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:56,217 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:56,218 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:56,218 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:56,219 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:56,219 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:56,220 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:56,220 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:56,220 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:56,221 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:56,221 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:56,222 #include "..." search starts here: 2023-09-12T11:06:56,222 #include <...> search starts here: 2023-09-12T11:06:56,223 /usr/include/eigen3 2023-09-12T11:06:56,223 include 2023-09-12T11:06:56,223 /usr/include/python3.11 2023-09-12T11:06:56,224 /usr/include/c++/12 2023-09-12T11:06:56,224 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:56,225 /usr/include/c++/12/backward 2023-09-12T11:06:56,225 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:56,226 /usr/local/include 2023-09-12T11:06:56,226 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:56,226 /usr/include 2023-09-12T11:06:56,227 End of search list. 2023-09-12T11:06:56,227 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:56,228 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:56,229 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:56,230 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:56,235 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:58,034 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:58,034 from include/openbabel/mol.h:43, 2023-09-12T11:06:58,034 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:58,035 from ./src/formats/mdlformat.cpp:26: 2023-09-12T11:06:58,036 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:58,036 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:58,037 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:58,038 | ^ 2023-09-12T11:06:58,038 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:58,039 37 | # define UNUSED(x) x 2023-09-12T11:06:58,040 | ^ 2023-09-12T11:06:58,733 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:58,734 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:58,734 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:58,735 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:58,736 | ^ 2023-09-12T11:06:58,736 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:58,737 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:58,738 | ^~~~~~~~ 2023-09-12T11:06:58,739 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:58,739 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:58,740 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:58,741 | ^ 2023-09-12T11:06:58,741 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:58,742 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:58,742 | ^~~~~~~~ 2023-09-12T11:06:58,757 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:58,758 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:58,758 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:58,759 | ^ 2023-09-12T11:06:58,760 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:58,760 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:58,761 | ^~~~~~~~ 2023-09-12T11:06:58,763 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:58,764 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:58,765 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:58,766 | ^ 2023-09-12T11:06:58,766 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:58,767 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:58,768 | ^~~~~~~~ 2023-09-12T11:06:58,937 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:58,938 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:58,938 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:58,939 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:58,940 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:58,940 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:58,941 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:58,942 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:58,943 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:58,944 from ./src/formats/mdlformat.cpp:22: 2023-09-12T11:06:58,944 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:58,945 131 | struct binary_function 2023-09-12T11:06:58,946 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:59,506 In file included from ./src/formats/mdlformat.cpp:34: 2023-09-12T11:06:59,506 include/formats/mdlvalence.h: In function ‘unsigned int MDLValence(unsigned int, int, unsigned int)’: 2023-09-12T11:06:59,507 include/formats/mdlvalence.h:51:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,508 51 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,508 | ^~ 2023-09-12T11:06:59,509 include/formats/mdlvalence.h:51:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,509 51 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,510 | ^~~~~ 2023-09-12T11:06:59,510 include/formats/mdlvalence.h:64:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,511 64 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,511 | ^~ 2023-09-12T11:06:59,515 include/formats/mdlvalence.h:64:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,515 64 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,516 | ^~~~~ 2023-09-12T11:06:59,516 include/formats/mdlvalence.h:77:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,517 77 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,517 | ^~ 2023-09-12T11:06:59,518 include/formats/mdlvalence.h:77:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,518 77 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,519 | ^~~~~ 2023-09-12T11:06:59,520 include/formats/mdlvalence.h:90:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,520 90 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,521 | ^~ 2023-09-12T11:06:59,522 include/formats/mdlvalence.h:90:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,523 90 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,523 | ^~~~~ 2023-09-12T11:06:59,524 include/formats/mdlvalence.h:103:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,524 103 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,525 | ^~ 2023-09-12T11:06:59,526 include/formats/mdlvalence.h:103:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,527 103 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,527 | ^~~~~ 2023-09-12T11:06:59,528 include/formats/mdlvalence.h:116:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,528 116 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,529 | ^~ 2023-09-12T11:06:59,530 include/formats/mdlvalence.h:116:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,530 116 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,531 | ^~~~~ 2023-09-12T11:06:59,532 include/formats/mdlvalence.h:119:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,533 119 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,533 | ^~ 2023-09-12T11:06:59,534 include/formats/mdlvalence.h:119:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,535 119 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,536 | ^~~~~ 2023-09-12T11:06:59,536 include/formats/mdlvalence.h:121:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,537 121 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,537 | ^~ 2023-09-12T11:06:59,538 include/formats/mdlvalence.h:121:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,538 121 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,539 | ^~~~~ 2023-09-12T11:06:59,539 include/formats/mdlvalence.h:134:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,540 134 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,541 | ^~ 2023-09-12T11:06:59,541 include/formats/mdlvalence.h:134:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,542 134 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,542 | ^~~~~ 2023-09-12T11:06:59,543 include/formats/mdlvalence.h:137:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,544 137 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,544 | ^~ 2023-09-12T11:06:59,545 include/formats/mdlvalence.h:137:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,546 137 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,546 | ^~~~~ 2023-09-12T11:06:59,547 include/formats/mdlvalence.h:139:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,548 139 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,549 | ^~ 2023-09-12T11:06:59,550 include/formats/mdlvalence.h:139:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,550 139 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,551 | ^~~~~ 2023-09-12T11:06:59,552 include/formats/mdlvalence.h:152:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,553 152 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,553 | ^~ 2023-09-12T11:06:59,554 include/formats/mdlvalence.h:152:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,555 152 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,555 | ^~~~~ 2023-09-12T11:06:59,556 include/formats/mdlvalence.h:155:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,557 155 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,557 | ^~ 2023-09-12T11:06:59,558 include/formats/mdlvalence.h:155:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,558 155 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,559 | ^~~~~ 2023-09-12T11:06:59,560 include/formats/mdlvalence.h:157:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,561 157 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,561 | ^~ 2023-09-12T11:06:59,562 include/formats/mdlvalence.h:157:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,563 157 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,563 | ^~~~~ 2023-09-12T11:06:59,564 include/formats/mdlvalence.h:170:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,564 170 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,565 | ^~ 2023-09-12T11:06:59,565 include/formats/mdlvalence.h:170:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,566 170 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,566 | ^~~~~ 2023-09-12T11:06:59,567 include/formats/mdlvalence.h:173:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,568 173 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,568 | ^~ 2023-09-12T11:06:59,569 include/formats/mdlvalence.h:173:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,569 173 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,570 | ^~~~~ 2023-09-12T11:06:59,570 include/formats/mdlvalence.h:175:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,571 175 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,571 | ^~ 2023-09-12T11:06:59,572 include/formats/mdlvalence.h:175:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,573 175 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,573 | ^~~~~ 2023-09-12T11:06:59,574 include/formats/mdlvalence.h:188:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,575 188 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,576 | ^~ 2023-09-12T11:06:59,576 include/formats/mdlvalence.h:188:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,577 188 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,578 | ^~~~~ 2023-09-12T11:06:59,579 include/formats/mdlvalence.h:191:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,580 191 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,581 | ^~ 2023-09-12T11:06:59,581 include/formats/mdlvalence.h:191:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,582 191 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,583 | ^~~~~ 2023-09-12T11:06:59,583 include/formats/mdlvalence.h:193:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,584 193 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,585 | ^~ 2023-09-12T11:06:59,585 include/formats/mdlvalence.h:193:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,586 193 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,587 | ^~~~~ 2023-09-12T11:06:59,587 include/formats/mdlvalence.h:206:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,588 206 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,589 | ^~ 2023-09-12T11:06:59,590 include/formats/mdlvalence.h:206:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,591 206 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,591 | ^~~~~ 2023-09-12T11:06:59,592 include/formats/mdlvalence.h:209:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,592 209 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,593 | ^~ 2023-09-12T11:06:59,593 include/formats/mdlvalence.h:209:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,594 209 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,594 | ^~~~~ 2023-09-12T11:06:59,595 include/formats/mdlvalence.h:211:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,596 211 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,596 | ^~ 2023-09-12T11:06:59,597 include/formats/mdlvalence.h:211:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,597 211 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,598 | ^~~~~ 2023-09-12T11:06:59,598 include/formats/mdlvalence.h:223:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,599 223 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,599 | ^~ 2023-09-12T11:06:59,600 include/formats/mdlvalence.h:223:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,601 223 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,601 | ^~~~~ 2023-09-12T11:06:59,602 include/formats/mdlvalence.h:226:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,603 226 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,604 | ^~ 2023-09-12T11:06:59,604 include/formats/mdlvalence.h:226:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,605 226 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,606 | ^~~~~ 2023-09-12T11:06:59,606 include/formats/mdlvalence.h:228:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,607 228 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,608 | ^~ 2023-09-12T11:06:59,609 include/formats/mdlvalence.h:228:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,609 228 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,610 | ^~~~~ 2023-09-12T11:06:59,611 include/formats/mdlvalence.h:240:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,611 240 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,612 | ^~ 2023-09-12T11:06:59,613 include/formats/mdlvalence.h:240:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,614 240 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,614 | ^~~~~ 2023-09-12T11:06:59,615 include/formats/mdlvalence.h:243:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,616 243 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,617 | ^~ 2023-09-12T11:06:59,617 include/formats/mdlvalence.h:243:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,618 243 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,619 | ^~~~~ 2023-09-12T11:06:59,619 include/formats/mdlvalence.h:245:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,620 245 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,620 | ^~ 2023-09-12T11:06:59,621 include/formats/mdlvalence.h:245:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,621 245 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,622 | ^~~~~ 2023-09-12T11:06:59,622 include/formats/mdlvalence.h:257:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,623 257 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,624 | ^~ 2023-09-12T11:06:59,624 include/formats/mdlvalence.h:257:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,625 257 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,625 | ^~~~~ 2023-09-12T11:06:59,626 include/formats/mdlvalence.h:260:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,626 260 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,627 | ^~ 2023-09-12T11:06:59,627 include/formats/mdlvalence.h:260:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,628 260 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,629 | ^~~~~ 2023-09-12T11:06:59,629 include/formats/mdlvalence.h:262:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,630 262 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,631 | ^~ 2023-09-12T11:06:59,631 include/formats/mdlvalence.h:262:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,632 262 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,633 | ^~~~~ 2023-09-12T11:06:59,634 include/formats/mdlvalence.h:274:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,634 274 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,635 | ^~ 2023-09-12T11:06:59,636 include/formats/mdlvalence.h:274:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,636 274 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,637 | ^~~~~ 2023-09-12T11:06:59,638 include/formats/mdlvalence.h:277:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,638 277 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,639 | ^~ 2023-09-12T11:06:59,640 include/formats/mdlvalence.h:277:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,640 277 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,641 | ^~~~~ 2023-09-12T11:06:59,642 include/formats/mdlvalence.h:279:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,643 279 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,643 | ^~ 2023-09-12T11:06:59,644 include/formats/mdlvalence.h:279:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,644 279 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,645 | ^~~~~ 2023-09-12T11:06:59,645 include/formats/mdlvalence.h:291:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,646 291 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,646 | ^~ 2023-09-12T11:06:59,647 include/formats/mdlvalence.h:291:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,647 291 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,648 | ^~~~~ 2023-09-12T11:06:59,648 include/formats/mdlvalence.h:294:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,649 294 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,649 | ^~ 2023-09-12T11:06:59,650 include/formats/mdlvalence.h:294:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,650 294 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,651 | ^~~~~ 2023-09-12T11:06:59,651 include/formats/mdlvalence.h:296:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,652 296 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,653 | ^~ 2023-09-12T11:06:59,653 include/formats/mdlvalence.h:296:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,654 296 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,655 | ^~~~~ 2023-09-12T11:06:59,655 include/formats/mdlvalence.h:298:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,656 298 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,657 | ^~ 2023-09-12T11:06:59,658 include/formats/mdlvalence.h:298:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,658 298 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,659 | ^~~~~ 2023-09-12T11:06:59,660 include/formats/mdlvalence.h:310:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,661 310 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,661 | ^~ 2023-09-12T11:06:59,662 include/formats/mdlvalence.h:310:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,662 310 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,663 | ^~~~~ 2023-09-12T11:06:59,664 include/formats/mdlvalence.h:313:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,665 313 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,665 | ^~ 2023-09-12T11:06:59,666 include/formats/mdlvalence.h:313:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,667 313 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,668 | ^~~~~ 2023-09-12T11:06:59,668 include/formats/mdlvalence.h:315:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,669 315 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,670 | ^~ 2023-09-12T11:06:59,670 include/formats/mdlvalence.h:315:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,671 315 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,672 | ^~~~~ 2023-09-12T11:06:59,672 include/formats/mdlvalence.h:317:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,673 317 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,673 | ^~ 2023-09-12T11:06:59,674 include/formats/mdlvalence.h:317:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,674 317 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,675 | ^~~~~ 2023-09-12T11:06:59,676 include/formats/mdlvalence.h:329:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,676 329 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,677 | ^~ 2023-09-12T11:06:59,677 include/formats/mdlvalence.h:329:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,678 329 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,678 | ^~~~~ 2023-09-12T11:06:59,679 include/formats/mdlvalence.h:332:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,680 332 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,681 | ^~ 2023-09-12T11:06:59,681 include/formats/mdlvalence.h:332:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,682 332 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,683 | ^~~~~ 2023-09-12T11:06:59,684 include/formats/mdlvalence.h:334:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,685 334 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,685 | ^~ 2023-09-12T11:06:59,686 include/formats/mdlvalence.h:334:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,687 334 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,688 | ^~~~~ 2023-09-12T11:06:59,688 include/formats/mdlvalence.h:336:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,689 336 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,690 | ^~ 2023-09-12T11:06:59,690 include/formats/mdlvalence.h:336:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,691 336 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,692 | ^~~~~ 2023-09-12T11:06:59,693 include/formats/mdlvalence.h:348:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,694 348 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,694 | ^~ 2023-09-12T11:06:59,695 include/formats/mdlvalence.h:348:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,696 348 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,697 | ^~~~~ 2023-09-12T11:06:59,698 include/formats/mdlvalence.h:351:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,698 351 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,699 | ^~ 2023-09-12T11:06:59,700 include/formats/mdlvalence.h:351:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,700 351 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,701 | ^~~~~ 2023-09-12T11:06:59,701 include/formats/mdlvalence.h:353:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,702 353 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,702 | ^~ 2023-09-12T11:06:59,703 include/formats/mdlvalence.h:353:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,704 353 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,704 | ^~~~~ 2023-09-12T11:06:59,705 include/formats/mdlvalence.h:355:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,706 355 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,706 | ^~ 2023-09-12T11:06:59,707 include/formats/mdlvalence.h:355:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,707 355 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,708 | ^~~~~ 2023-09-12T11:06:59,709 include/formats/mdlvalence.h:367:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,709 367 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,710 | ^~ 2023-09-12T11:06:59,711 include/formats/mdlvalence.h:367:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,711 367 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,712 | ^~~~~ 2023-09-12T11:06:59,713 include/formats/mdlvalence.h:370:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,713 370 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,714 | ^~ 2023-09-12T11:06:59,715 include/formats/mdlvalence.h:370:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,716 370 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,716 | ^~~~~ 2023-09-12T11:06:59,717 include/formats/mdlvalence.h:372:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,718 372 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,718 | ^~ 2023-09-12T11:06:59,719 include/formats/mdlvalence.h:372:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,720 372 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,720 | ^~~~~ 2023-09-12T11:06:59,721 include/formats/mdlvalence.h:374:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,722 374 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,722 | ^~ 2023-09-12T11:06:59,723 include/formats/mdlvalence.h:374:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,724 374 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,725 | ^~~~~ 2023-09-12T11:06:59,725 include/formats/mdlvalence.h:385:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,726 385 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,726 | ^~ 2023-09-12T11:06:59,727 include/formats/mdlvalence.h:385:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,727 385 | if (val <= 7) return 7; break; 2023-09-12T11:06:59,728 | ^~~~~ 2023-09-12T11:06:59,728 include/formats/mdlvalence.h:388:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,729 388 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,730 | ^~ 2023-09-12T11:06:59,730 include/formats/mdlvalence.h:388:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,731 388 | if (val <= 6) return 6; break; 2023-09-12T11:06:59,731 | ^~~~~ 2023-09-12T11:06:59,732 include/formats/mdlvalence.h:390:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,733 390 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,733 | ^~ 2023-09-12T11:06:59,734 include/formats/mdlvalence.h:390:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,734 390 | if (val <= 5) return 5; break; 2023-09-12T11:06:59,735 | ^~~~~ 2023-09-12T11:06:59,736 include/formats/mdlvalence.h:392:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,736 392 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,737 | ^~ 2023-09-12T11:06:59,738 include/formats/mdlvalence.h:392:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,738 392 | if (val <= 4) return 4; break; 2023-09-12T11:06:59,739 | ^~~~~ 2023-09-12T11:06:59,740 include/formats/mdlvalence.h:394:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:06:59,740 394 | if (val <= 3) return 3; break; 2023-09-12T11:06:59,741 | ^~ 2023-09-12T11:06:59,742 include/formats/mdlvalence.h:394:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:06:59,742 394 | if (val <= 3) return 3; break; 2023-09-12T11:06:59,743 | ^~~~~ 2023-09-12T11:06:59,744 include/formats/mdlvalence.h: In function ‘unsigned int HYDValence(unsigned int, int, unsigned int)’: 2023-09-12T11:06:59,744 include/formats/mdlvalence.h:416:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:06:59,745 416 | if (val > impval) { 2023-09-12T11:06:59,745 | ~~~~^~~~~~~~ 2023-09-12T11:07:00,019 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadV3000Block(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, bool)’: 2023-09-12T11:07:00,020 ./src/formats/mdlformat.cpp:1273:85: warning: unused parameter ‘DoMany’ [-Wunused-parameter] 2023-09-12T11:07:00,021 1273 | bool MDLFormat::ReadV3000Block(istream& ifs, OBMol& mol, OBConversion* pConv,bool DoMany) 2023-09-12T11:07:00,021 | ~~~~~^~~~~~ 2023-09-12T11:07:00,037 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadAtomBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:07:00,037 ./src/formats/mdlformat.cpp:1341:10: warning: unused variable ‘chiralWatch’ [-Wunused-variable] 2023-09-12T11:07:00,038 1341 | bool chiralWatch=false; 2023-09-12T11:07:00,039 | ^~~~~~~~~~~ 2023-09-12T11:07:00,039 ./src/formats/mdlformat.cpp:1338:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:07:00,040 1338 | bool MDLFormat::ReadAtomBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:07:00,040 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:07:00,043 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadBondBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:07:00,043 ./src/formats/mdlformat.cpp:1422:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:07:00,044 1422 | bool MDLFormat::ReadBondBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:07:00,045 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:07:00,045 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadUnimplementedBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, std::string&)’: 2023-09-12T11:07:00,046 ./src/formats/mdlformat.cpp:1481:62: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T11:07:00,046 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2023-09-12T11:07:00,047 | ~~~~~~~^~~ 2023-09-12T11:07:00,048 ./src/formats/mdlformat.cpp:1481:81: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:07:00,049 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2023-09-12T11:07:00,049 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:07:00,050 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadRGroupBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:07:00,051 ./src/formats/mdlformat.cpp:1497:55: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T11:07:00,052 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:07:00,052 | ~~~~~~~^~~ 2023-09-12T11:07:00,053 ./src/formats/mdlformat.cpp:1497:74: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:07:00,054 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:07:00,055 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:07:00,074 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::WriteV3000(std::ostream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:07:00,075 ./src/formats/mdlformat.cpp:1514:69: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:07:00,076 1514 | bool MDLFormat::WriteV3000(ostream& ofs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:07:00,076 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:07:00,181 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2023-09-12T11:07:00,182 ./src/formats/mdlformat.cpp:1957:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:07:00,183 1957 | unsigned int second = (a1_b2 == NULL) ? OBStereo::ImplicitRef : a1_b2->GetNbrAtom(a1)->GetId(); 2023-09-12T11:07:00,184 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:00,185 ./src/formats/mdlformat.cpp:1958:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:07:00,186 1958 | unsigned int fourth = (a2_b2 == NULL) ? OBStereo::ImplicitRef : a2_b2->GetNbrAtom(a2)->GetId(); 2023-09-12T11:07:00,186 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:02,320 ./src/formats/mdlformat.cpp: In member function ‘virtual bool OpenBabel::MDLFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:02,320 ./src/formats/mdlformat.cpp:527:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T11:07:02,321 527 | flag |= OBBond::CisOrTrans; 2023-09-12T11:07:02,321 | ~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:02,322 ./src/formats/mdlformat.cpp:528:15: note: here 2023-09-12T11:07:02,322 528 | case 4: 2023-09-12T11:07:02,323 | ^~~~ 2023-09-12T11:07:08,559 ./src/formats/mdlformat.cpp: In member function ‘std::string OpenBabel::MDLFormat::GetTimeDate()’: 2023-09-12T11:07:08,559 ./src/formats/mdlformat.cpp:1648:31: warning: ‘%02d’ directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 7 [-Wformat-truncation=] 2023-09-12T11:07:08,560 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2023-09-12T11:07:08,561 | ^~~~ 2023-09-12T11:07:08,561 ./src/formats/mdlformat.cpp:1648:22: note: directive argument in the range [-2147483648, 2147483547] 2023-09-12T11:07:08,562 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2023-09-12T11:07:08,562 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:08,563 ./src/formats/mdlformat.cpp:1648:13: note: ‘snprintf’ output between 11 and 56 bytes into a destination of size 11 2023-09-12T11:07:08,564 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2023-09-12T11:07:08,565 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:08,565 1649 | ((ts->tm_year>=100)? ts->tm_year-100 : ts->tm_year), 2023-09-12T11:07:08,566 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:08,567 1650 | ts->tm_hour, ts->tm_min); 2023-09-12T11:07:08,567 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:09,350 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2023-09-12T11:07:09,350 ./src/formats/mdlformat.cpp:1967:58: warning: ‘a2_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:07:09,351 1967 | if (a1_stereo == OBStereo::UnknownDir || a2_stereo == OBStereo::UnknownDir) 2023-09-12T11:07:09,352 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:09,353 ./src/formats/mdlformat.cpp:1926:42: note: ‘a2_stereo’ was declared here 2023-09-12T11:07:09,353 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2023-09-12T11:07:09,354 | ^~~~~~~~~ 2023-09-12T11:07:09,354 ./src/formats/mdlformat.cpp:1967:21: warning: ‘a1_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:07:09,355 1967 | if (a1_stereo == OBStereo::UnknownDir || a2_stereo == OBStereo::UnknownDir) 2023-09-12T11:07:09,356 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:09,356 ./src/formats/mdlformat.cpp:1926:31: note: ‘a1_stereo’ was declared here 2023-09-12T11:07:09,357 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2023-09-12T11:07:09,358 | ^~~~~~~~~ 2023-09-12T11:07:19,932 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:19,933 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mdlformat.o /tmp/ccuu4BYh.s 2023-09-12T11:07:19,938 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:21,374 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:07:21,374 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:07:21,375 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mdlformat.' 2023-09-12T11:07:21,381 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mmcifformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mmcifformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:07:21,384 Using built-in specs. 2023-09-12T11:07:21,385 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:21,386 Target: arm-linux-gnueabihf 2023-09-12T11:07:21,386 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:07:21,387 Thread model: posix 2023-09-12T11:07:21,388 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:21,388 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:21,389 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmcifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:21,389 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mmcifformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mmcifformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cczgbzdi.s 2023-09-12T11:07:21,398 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:21,398 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:21,399 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:21,400 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:21,400 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:21,401 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:21,401 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:21,402 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:21,403 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:21,403 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:21,404 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:21,405 #include "..." search starts here: 2023-09-12T11:07:21,405 #include <...> search starts here: 2023-09-12T11:07:21,406 /usr/include/eigen3 2023-09-12T11:07:21,407 include 2023-09-12T11:07:21,407 /usr/include/python3.11 2023-09-12T11:07:21,408 /usr/include/c++/12 2023-09-12T11:07:21,409 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:21,409 /usr/include/c++/12/backward 2023-09-12T11:07:21,410 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:21,411 /usr/local/include 2023-09-12T11:07:21,411 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:21,412 /usr/include 2023-09-12T11:07:21,412 End of search list. 2023-09-12T11:07:21,413 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:21,413 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:21,415 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:21,415 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:21,416 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:22,985 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:22,986 from include/openbabel/mol.h:43, 2023-09-12T11:07:22,987 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:22,988 from ./src/formats/mmcifformat.cpp:19: 2023-09-12T11:07:22,988 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:22,989 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:22,990 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:22,991 | ^ 2023-09-12T11:07:22,991 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:22,992 37 | # define UNUSED(x) x 2023-09-12T11:07:22,993 | ^ 2023-09-12T11:07:23,756 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:23,756 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,757 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,757 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:23,758 | ^ 2023-09-12T11:07:23,758 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:23,759 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:23,760 | ^~~~~~~~ 2023-09-12T11:07:23,761 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,761 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,762 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:23,763 | ^ 2023-09-12T11:07:23,764 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:23,764 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:23,765 | ^~~~~~~~ 2023-09-12T11:07:23,780 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,781 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,781 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:23,782 | ^ 2023-09-12T11:07:23,783 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:23,784 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:23,784 | ^~~~~~~~ 2023-09-12T11:07:23,786 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,787 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,787 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:23,788 | ^ 2023-09-12T11:07:23,789 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:23,790 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:23,791 | ^~~~~~~~ 2023-09-12T11:07:23,959 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:23,960 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:23,960 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:23,961 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:23,961 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:23,962 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:23,962 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:23,963 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:23,964 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:23,964 from include/openbabel/mol.h:35: 2023-09-12T11:07:23,965 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:23,965 131 | struct binary_function 2023-09-12T11:07:23,966 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:26,019 ./src/formats/mmcifformat.cpp: In member function ‘bool OpenBabel::CIFLexer::next_token(Token&)’: 2023-09-12T11:07:26,020 ./src/formats/mmcifformat.cpp:394:8: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T11:07:26,020 394 | if (last_char == '\n') 2023-09-12T11:07:26,021 | ^~ 2023-09-12T11:07:26,022 ./src/formats/mmcifformat.cpp:421:6: note: here 2023-09-12T11:07:26,022 421 | default: // reading an un-quoted text string 2023-09-12T11:07:26,023 | ^~~~~~~ 2023-09-12T11:07:26,029 ./src/formats/mmcifformat.cpp: In member function ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:26,030 ./src/formats/mmcifformat.cpp:638:16: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T11:07:26,030 638 | if(string::npos != token.as_text.find_first_of("0123456789")) 2023-09-12T11:07:26,031 | ^~ 2023-09-12T11:07:26,032 ./src/formats/mmcifformat.cpp:640:14: note: here 2023-09-12T11:07:26,033 640 | case CIFTagID::_atom_site_type_symbol: 2023-09-12T11:07:26,033 | ^~~~ 2023-09-12T11:07:31,664 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:07:31,664 from include/openbabel/mol.h:37: 2023-09-12T11:07:31,665 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: 2023-09-12T11:07:31,666 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:07:31,666 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:07:31,667 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:32,766 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:07:32,767 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:07:32,768 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:846:41: 2023-09-12T11:07:32,768 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:07:32,769 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:07:32,770 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:32,770 512 | std::tuple(__k), 2023-09-12T11:07:32,771 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:32,772 513 | std::tuple<>()); 2023-09-12T11:07:32,773 | ~~~~~~~~~~~~~~~ 2023-09-12T11:07:32,773 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, 2023-09-12T11:07:32,774 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:981:66: 2023-09-12T11:07:32,775 /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2023-09-12T11:07:32,776 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:07:32,777 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:32,778 512 | std::tuple(__k), 2023-09-12T11:07:32,779 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:32,780 513 | std::tuple<>()); 2023-09-12T11:07:32,781 | ~~~~~~~~~~~~~~~ 2023-09-12T11:07:35,235 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmcifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:35,236 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mmcifformat.o /tmp/cczgbzdi.s 2023-09-12T11:07:35,243 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:36,037 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:07:36,037 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:07:36,038 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmcifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmcifformat.' 2023-09-12T11:07:36,041 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mmodformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mmodformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:07:36,045 Using built-in specs. 2023-09-12T11:07:36,046 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:36,047 Target: arm-linux-gnueabihf 2023-09-12T11:07:36,047 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:07:36,048 Thread model: posix 2023-09-12T11:07:36,049 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:36,049 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:36,050 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmodformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:36,050 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mmodformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mmodformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccNSXVG4.s 2023-09-12T11:07:36,059 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:36,060 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:36,061 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:36,062 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:36,062 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:36,063 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:36,063 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:36,064 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:36,064 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:36,065 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:36,065 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:36,065 #include "..." search starts here: 2023-09-12T11:07:36,066 #include <...> search starts here: 2023-09-12T11:07:36,066 /usr/include/eigen3 2023-09-12T11:07:36,067 include 2023-09-12T11:07:36,068 /usr/include/python3.11 2023-09-12T11:07:36,068 /usr/include/c++/12 2023-09-12T11:07:36,069 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:36,070 /usr/include/c++/12/backward 2023-09-12T11:07:36,070 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:36,071 /usr/local/include 2023-09-12T11:07:36,072 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:36,072 /usr/include 2023-09-12T11:07:36,073 End of search list. 2023-09-12T11:07:36,074 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:36,074 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:36,076 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:36,076 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:36,077 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:37,649 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:37,650 from include/openbabel/mol.h:43, 2023-09-12T11:07:37,651 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:37,651 from ./src/formats/mmodformat.cpp:17: 2023-09-12T11:07:37,652 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:37,653 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:37,653 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:37,654 | ^ 2023-09-12T11:07:37,655 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:37,655 37 | # define UNUSED(x) x 2023-09-12T11:07:37,656 | ^ 2023-09-12T11:07:38,420 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:38,420 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:38,421 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:38,422 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:38,423 | ^ 2023-09-12T11:07:38,424 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:38,424 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:38,425 | ^~~~~~~~ 2023-09-12T11:07:38,425 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:38,426 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:38,426 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:38,427 | ^ 2023-09-12T11:07:38,428 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:38,428 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:38,429 | ^~~~~~~~ 2023-09-12T11:07:38,444 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:38,445 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:38,445 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:38,446 | ^ 2023-09-12T11:07:38,446 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:38,447 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:38,448 | ^~~~~~~~ 2023-09-12T11:07:38,450 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:38,451 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:38,452 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:38,453 | ^ 2023-09-12T11:07:38,453 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:38,454 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:38,455 | ^~~~~~~~ 2023-09-12T11:07:38,625 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:38,626 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:38,627 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:38,628 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:38,628 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:38,629 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:38,630 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:38,631 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:38,632 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:38,632 from include/openbabel/mol.h:35: 2023-09-12T11:07:38,633 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:38,633 131 | struct binary_function 2023-09-12T11:07:38,634 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:42,333 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmodformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:42,334 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mmodformat.o /tmp/ccNSXVG4.s 2023-09-12T11:07:42,338 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:42,567 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:07:42,568 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:07:42,568 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmodformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mmodformat.' 2023-09-12T11:07:42,569 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mol2format.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mol2format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:07:42,573 Using built-in specs. 2023-09-12T11:07:42,574 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:42,575 Target: arm-linux-gnueabihf 2023-09-12T11:07:42,575 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:07:42,576 Thread model: posix 2023-09-12T11:07:42,576 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:42,577 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:42,577 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mol2format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:42,578 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mol2format.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mol2format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccygX0xX.s 2023-09-12T11:07:42,586 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:42,587 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:42,588 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:42,588 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:42,589 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:42,589 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:42,590 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:42,590 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:42,591 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:42,592 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:42,592 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:42,593 #include "..." search starts here: 2023-09-12T11:07:42,594 #include <...> search starts here: 2023-09-12T11:07:42,594 /usr/include/eigen3 2023-09-12T11:07:42,595 include 2023-09-12T11:07:42,595 /usr/include/python3.11 2023-09-12T11:07:42,596 /usr/include/c++/12 2023-09-12T11:07:42,596 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:42,597 /usr/include/c++/12/backward 2023-09-12T11:07:42,597 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:42,598 /usr/local/include 2023-09-12T11:07:42,598 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:42,599 /usr/include 2023-09-12T11:07:42,599 End of search list. 2023-09-12T11:07:42,600 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:42,600 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:42,601 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:42,602 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:42,605 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:44,175 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:44,175 from include/openbabel/mol.h:43, 2023-09-12T11:07:44,176 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:44,177 from ./src/formats/mol2format.cpp:17: 2023-09-12T11:07:44,177 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:44,178 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:44,178 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:44,179 | ^ 2023-09-12T11:07:44,179 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:44,180 37 | # define UNUSED(x) x 2023-09-12T11:07:44,180 | ^ 2023-09-12T11:07:44,947 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:44,947 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:44,948 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:44,948 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:44,949 | ^ 2023-09-12T11:07:44,950 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:44,950 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:44,951 | ^~~~~~~~ 2023-09-12T11:07:44,952 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:44,953 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:44,953 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:44,954 | ^ 2023-09-12T11:07:44,955 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:44,956 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:44,956 | ^~~~~~~~ 2023-09-12T11:07:44,971 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:44,972 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:44,972 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:44,973 | ^ 2023-09-12T11:07:44,974 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:44,974 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:44,975 | ^~~~~~~~ 2023-09-12T11:07:44,977 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:44,978 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:44,979 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:44,980 | ^ 2023-09-12T11:07:44,981 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:44,981 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:44,982 | ^~~~~~~~ 2023-09-12T11:07:45,151 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:45,151 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:45,152 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:45,152 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:45,153 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:45,154 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:45,154 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:45,155 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:45,155 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:45,156 from include/openbabel/mol.h:35: 2023-09-12T11:07:45,157 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:45,157 131 | struct binary_function 2023-09-12T11:07:45,158 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:45,351 ./src/formats/mol2format.cpp: In member function ‘virtual const char* OpenBabel::MOL2Format::Description()’: 2023-09-12T11:07:45,352 ./src/formats/mol2format.cpp:49:9: warning: statement has no effect [-Wunused-value] 2023-09-12T11:07:45,352 49 | " c Write UCSF Dock scores saved in comments preceeding molecules\n\n"; 2023-09-12T11:07:45,353 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:45,384 ./src/formats/mol2format.cpp: In member function ‘virtual bool OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:45,384 ./src/formats/mol2format.cpp:391:46: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:07:45,385 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2023-09-12T11:07:45,386 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:07:45,387 ./src/formats/mol2format.cpp:391:87: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:07:45,387 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2023-09-12T11:07:45,388 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:07:45,389 ./src/formats/mol2format.cpp:394:51: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:07:45,390 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2023-09-12T11:07:45,390 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:07:45,391 ./src/formats/mol2format.cpp:394:92: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:07:45,392 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2023-09-12T11:07:45,392 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:07:45,393 ./src/formats/mol2format.cpp:476:99: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:07:45,394 476 | if (n_h_bonded < min_n_h_bonded || (n_h_bonded == min_n_h_bonded && partner->GetIdx() < min_idx)) { 2023-09-12T11:07:45,394 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:07:45,395 ./src/formats/mol2format.cpp:499:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:07:45,395 499 | if (partner->GetIdx() == min_idx) { 2023-09-12T11:07:45,396 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:07:45,425 ./src/formats/mol2format.cpp: In member function ‘virtual int OpenBabel::MOL2Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:07:45,425 ./src/formats/mol2format.cpp:727:10: warning: unused variable ‘ch’ [-Wunused-variable] 2023-09-12T11:07:45,426 727 | char ch = ifs.peek(); 2023-09-12T11:07:45,426 | ^~ 2023-09-12T11:07:51,031 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mol2format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:51,031 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mol2format.o /tmp/ccygX0xX.s 2023-09-12T11:07:51,036 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:51,429 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:07:51,429 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:07:51,432 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mol2format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mol2format.' 2023-09-12T11:07:51,433 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/moldenformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/moldenformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:07:51,438 Using built-in specs. 2023-09-12T11:07:51,438 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:51,439 Target: arm-linux-gnueabihf 2023-09-12T11:07:51,440 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:07:51,441 Thread model: posix 2023-09-12T11:07:51,442 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:51,442 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:51,443 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/moldenformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:07:51,444 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/moldenformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase moldenformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccEXHbUk.s 2023-09-12T11:07:51,453 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:51,454 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:51,455 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:51,456 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:51,457 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:51,457 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:51,458 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:51,459 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:51,460 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:51,461 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:51,462 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:51,463 #include "..." search starts here: 2023-09-12T11:07:51,464 #include <...> search starts here: 2023-09-12T11:07:51,465 /usr/include/eigen3 2023-09-12T11:07:51,466 include 2023-09-12T11:07:51,468 /usr/include/python3.11 2023-09-12T11:07:51,469 /usr/include/c++/12 2023-09-12T11:07:51,471 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:51,472 /usr/include/c++/12/backward 2023-09-12T11:07:51,474 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:51,475 /usr/local/include 2023-09-12T11:07:51,477 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:51,480 /usr/include 2023-09-12T11:07:51,482 End of search list. 2023-09-12T11:07:51,484 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:51,486 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:51,490 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:51,492 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:51,494 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:53,143 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:53,143 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:53,144 from ./src/formats/moldenformat.cpp:35: 2023-09-12T11:07:53,145 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:53,146 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:53,146 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:53,147 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:07:53,148 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:07:53,149 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:07:53,150 from /usr/include/c++/12/ios:42, 2023-09-12T11:07:53,150 from /usr/include/c++/12/istream:38, 2023-09-12T11:07:53,151 from /usr/include/c++/12/fstream:38, 2023-09-12T11:07:53,152 from ./src/formats/moldenformat.cpp:27: 2023-09-12T11:07:53,153 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:53,154 131 | struct binary_function 2023-09-12T11:07:53,155 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:53,372 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:53,373 from include/openbabel/mol.h:43, 2023-09-12T11:07:53,374 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:53,375 from ./src/formats/moldenformat.cpp:36: 2023-09-12T11:07:53,376 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:53,377 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:53,378 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:53,379 | ^ 2023-09-12T11:07:53,380 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:53,381 37 | # define UNUSED(x) x 2023-09-12T11:07:53,382 | ^ 2023-09-12T11:07:54,046 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:54,046 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:54,047 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:54,048 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:54,048 | ^ 2023-09-12T11:07:54,049 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:54,050 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:54,051 | ^~~~~~~~ 2023-09-12T11:07:54,052 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:54,052 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:54,053 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:54,053 | ^ 2023-09-12T11:07:54,054 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:54,055 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:54,055 | ^~~~~~~~ 2023-09-12T11:07:54,072 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:54,072 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:54,073 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:54,073 | ^ 2023-09-12T11:07:54,074 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:54,075 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:54,075 | ^~~~~~~~ 2023-09-12T11:07:54,078 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:54,079 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:54,079 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:54,080 | ^ 2023-09-12T11:07:54,081 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:54,081 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:54,082 | ^~~~~~~~ 2023-09-12T11:07:54,330 ./src/formats/moldenformat.cpp: In member function ‘virtual int OpenBabel::OBMoldenFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:07:54,331 ./src/formats/moldenformat.cpp:85:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:07:54,332 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:07:54,333 | ~~~~^ 2023-09-12T11:07:54,333 ./src/formats/moldenformat.cpp:85:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:07:54,334 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:07:54,335 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:07:54,344 ./src/formats/moldenformat.cpp: In member function ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:54,345 ./src/formats/moldenformat.cpp:171:48: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:07:54,345 171 | if (sscanf(lineBuffer.c_str(), "%d", &natoms) == 0 || !natoms) { 2023-09-12T11:07:54,346 | ~^ ~~~~~~~ 2023-09-12T11:07:54,347 | | | 2023-09-12T11:07:54,347 | | unsigned int* 2023-09-12T11:07:54,348 | int* 2023-09-12T11:07:54,349 | %d 2023-09-12T11:07:57,504 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:07:57,504 from ./src/formats/moldenformat.cpp:29: 2023-09-12T11:07:57,505 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:07:57,506 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:07:57,506 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:07:57,507 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:57,564 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::vector3&}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:07:57,565 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:07:57,635 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:07:57,636 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:07:59,169 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:07:59,169 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:07:59,170 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:192:33: 2023-09-12T11:07:59,171 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:07:59,171 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:59,172 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:59,173 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:07:59,173 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:208:38: 2023-09-12T11:07:59,174 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:07:59,175 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:59,175 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:59,176 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:07:59,177 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:240:36: 2023-09-12T11:07:59,178 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:07:59,178 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:59,179 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:59,180 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:07:59,180 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:251:36: 2023-09-12T11:07:59,181 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:07:59,181 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:59,182 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:59,183 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:07:59,183 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:07:59,184 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:290:32: 2023-09-12T11:07:59,184 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:07:59,185 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:07:59,186 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:01,371 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/moldenformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:01,371 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/moldenformat.o /tmp/ccEXHbUk.s 2023-09-12T11:08:01,376 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:01,896 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:01,897 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:01,897 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/moldenformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/moldenformat.' 2023-09-12T11:08:01,900 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/molproformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/molproformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:01,904 Using built-in specs. 2023-09-12T11:08:01,905 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:01,905 Target: arm-linux-gnueabihf 2023-09-12T11:08:01,906 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:01,906 Thread model: posix 2023-09-12T11:08:01,907 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:01,907 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:01,908 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/molproformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:01,908 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/molproformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase molproformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccneNdbv.s 2023-09-12T11:08:01,917 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:01,918 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:01,919 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:01,919 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:01,920 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:01,921 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:01,921 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:01,922 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:01,922 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:01,923 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:01,924 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:01,924 #include "..." search starts here: 2023-09-12T11:08:01,925 #include <...> search starts here: 2023-09-12T11:08:01,925 /usr/include/eigen3 2023-09-12T11:08:01,925 include 2023-09-12T11:08:01,926 /usr/include/python3.11 2023-09-12T11:08:01,926 /usr/include/c++/12 2023-09-12T11:08:01,926 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:01,927 /usr/include/c++/12/backward 2023-09-12T11:08:01,927 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:01,928 /usr/local/include 2023-09-12T11:08:01,928 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:01,929 /usr/include 2023-09-12T11:08:01,929 End of search list. 2023-09-12T11:08:01,929 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:01,930 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:01,931 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:01,931 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:01,935 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:03,506 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:03,506 from include/openbabel/mol.h:43, 2023-09-12T11:08:03,507 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:03,508 from ./src/formats/molproformat.cpp:20: 2023-09-12T11:08:03,508 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:03,509 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:03,509 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:03,510 | ^ 2023-09-12T11:08:03,511 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:03,511 37 | # define UNUSED(x) x 2023-09-12T11:08:03,512 | ^ 2023-09-12T11:08:04,276 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:04,277 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:04,278 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:04,278 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:04,279 | ^ 2023-09-12T11:08:04,280 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:04,280 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:04,281 | ^~~~~~~~ 2023-09-12T11:08:04,282 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:04,282 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:04,283 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:04,284 | ^ 2023-09-12T11:08:04,284 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:04,285 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:04,286 | ^~~~~~~~ 2023-09-12T11:08:04,300 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:04,301 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:04,302 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:04,302 | ^ 2023-09-12T11:08:04,303 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:04,303 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:04,304 | ^~~~~~~~ 2023-09-12T11:08:04,307 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:04,308 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:04,308 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:04,309 | ^ 2023-09-12T11:08:04,309 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:04,310 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:04,311 | ^~~~~~~~ 2023-09-12T11:08:04,480 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:04,481 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:04,481 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:04,482 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:04,483 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:04,484 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:04,484 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:04,485 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:04,486 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:04,486 from include/openbabel/mol.h:35: 2023-09-12T11:08:04,487 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:04,488 131 | struct binary_function 2023-09-12T11:08:04,488 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:07,778 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:08:07,779 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:08:07,779 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:07,780 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:08:07,781 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:07,829 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:08:07,830 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:08,017 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:08:08,018 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:08,644 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,644 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:08,645 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:189:33: 2023-09-12T11:08:08,645 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,646 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:08,647 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:08,647 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,648 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:08,649 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:191:33: 2023-09-12T11:08:08,650 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,650 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:08,651 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:08,652 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,653 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:08,653 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:198:33: 2023-09-12T11:08:08,654 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,655 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:08,655 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:08,656 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,657 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:08,657 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:206:28: 2023-09-12T11:08:08,658 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,659 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:08,659 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:08,660 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,660 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:08,661 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:210:28: 2023-09-12T11:08:08,661 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,662 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:08,662 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:08,663 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,664 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:08,665 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:214:28: 2023-09-12T11:08:08,665 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,666 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:08,667 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:08,668 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:08:08,668 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:08,669 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:217:33: 2023-09-12T11:08:08,670 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,670 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:08,671 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:08,672 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:08:08,672 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,673 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:223:29: 2023-09-12T11:08:08,674 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,674 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:08:08,675 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:08:08,676 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:08,677 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:224:36: 2023-09-12T11:08:08,677 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:08,678 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:08:08,678 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:08:09,901 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/molproformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:09,902 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/molproformat.o /tmp/ccneNdbv.s 2023-09-12T11:08:09,907 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:10,290 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:10,291 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:10,291 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/molproformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/molproformat.' 2023-09-12T11:08:10,293 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/molreport.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/molreport.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:10,297 Using built-in specs. 2023-09-12T11:08:10,298 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:10,299 Target: arm-linux-gnueabihf 2023-09-12T11:08:10,299 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:10,300 Thread model: posix 2023-09-12T11:08:10,300 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:10,301 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:10,301 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/molreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:10,302 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/molreport.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase molreport.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccxWBwWp.s 2023-09-12T11:08:10,310 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:10,311 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:10,312 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:10,312 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:10,313 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:10,314 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:10,314 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:10,315 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:10,316 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:10,316 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:10,317 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:10,317 #include "..." search starts here: 2023-09-12T11:08:10,318 #include <...> search starts here: 2023-09-12T11:08:10,319 /usr/include/eigen3 2023-09-12T11:08:10,319 include 2023-09-12T11:08:10,320 /usr/include/python3.11 2023-09-12T11:08:10,320 /usr/include/c++/12 2023-09-12T11:08:10,321 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:10,321 /usr/include/c++/12/backward 2023-09-12T11:08:10,322 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:10,323 /usr/local/include 2023-09-12T11:08:10,323 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:10,324 /usr/include 2023-09-12T11:08:10,325 End of search list. 2023-09-12T11:08:10,325 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:10,326 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:10,327 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:10,328 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:10,330 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:11,895 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:11,896 from include/openbabel/mol.h:43, 2023-09-12T11:08:11,896 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:11,897 from ./src/formats/molreport.cpp:21: 2023-09-12T11:08:11,897 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:11,898 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:11,898 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:11,899 | ^ 2023-09-12T11:08:11,899 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:11,900 37 | # define UNUSED(x) x 2023-09-12T11:08:11,900 | ^ 2023-09-12T11:08:12,665 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:12,666 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:12,667 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:12,667 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:12,668 | ^ 2023-09-12T11:08:12,669 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:12,669 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:12,670 | ^~~~~~~~ 2023-09-12T11:08:12,671 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:12,672 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:12,672 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:12,673 | ^ 2023-09-12T11:08:12,674 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:12,674 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:12,675 | ^~~~~~~~ 2023-09-12T11:08:12,690 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:12,690 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:12,691 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:12,692 | ^ 2023-09-12T11:08:12,692 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:12,693 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:12,694 | ^~~~~~~~ 2023-09-12T11:08:12,696 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:12,697 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:12,697 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:12,698 | ^ 2023-09-12T11:08:12,698 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:12,699 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:12,700 | ^~~~~~~~ 2023-09-12T11:08:12,869 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:12,869 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:12,870 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:12,871 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:12,871 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:12,872 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:12,872 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:12,873 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:12,874 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:12,874 from include/openbabel/mol.h:35: 2023-09-12T11:08:12,875 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:12,875 131 | struct binary_function 2023-09-12T11:08:12,876 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:15,291 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/molreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:15,292 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/molreport.o /tmp/ccxWBwWp.s 2023-09-12T11:08:15,297 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:15,438 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:15,439 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:15,439 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/molreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/molreport.' 2023-09-12T11:08:15,441 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mopacformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mopacformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:15,445 Using built-in specs. 2023-09-12T11:08:15,446 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:15,446 Target: arm-linux-gnueabihf 2023-09-12T11:08:15,447 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:15,447 Thread model: posix 2023-09-12T11:08:15,448 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:15,448 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:15,449 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mopacformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:15,449 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mopacformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mopacformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccHOM5Af.s 2023-09-12T11:08:15,459 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:15,459 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:15,460 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:15,461 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:15,462 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:15,462 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:15,463 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:15,463 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:15,464 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:15,464 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:15,465 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:15,465 #include "..." search starts here: 2023-09-12T11:08:15,466 #include <...> search starts here: 2023-09-12T11:08:15,466 /usr/include/eigen3 2023-09-12T11:08:15,466 include 2023-09-12T11:08:15,467 /usr/include/python3.11 2023-09-12T11:08:15,467 /usr/include/c++/12 2023-09-12T11:08:15,468 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:15,468 /usr/include/c++/12/backward 2023-09-12T11:08:15,468 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:15,469 /usr/local/include 2023-09-12T11:08:15,469 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:15,470 /usr/include 2023-09-12T11:08:15,470 End of search list. 2023-09-12T11:08:15,471 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:15,471 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:15,472 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:15,472 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:15,477 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:17,043 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:17,044 from include/openbabel/mol.h:43, 2023-09-12T11:08:17,044 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:17,045 from ./src/formats/mopacformat.cpp:17: 2023-09-12T11:08:17,046 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:17,047 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:17,047 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:17,048 | ^ 2023-09-12T11:08:17,049 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:17,050 37 | # define UNUSED(x) x 2023-09-12T11:08:17,050 | ^ 2023-09-12T11:08:17,811 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:17,812 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:17,813 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:17,814 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:17,814 | ^ 2023-09-12T11:08:17,815 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:17,816 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:17,816 | ^~~~~~~~ 2023-09-12T11:08:17,817 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:17,818 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:17,819 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:17,819 | ^ 2023-09-12T11:08:17,820 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:17,821 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:17,822 | ^~~~~~~~ 2023-09-12T11:08:17,836 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:17,836 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:17,837 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:17,837 | ^ 2023-09-12T11:08:17,838 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:17,839 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:17,839 | ^~~~~~~~ 2023-09-12T11:08:17,842 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:17,843 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:17,843 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:17,844 | ^ 2023-09-12T11:08:17,844 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:17,845 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:17,846 | ^~~~~~~~ 2023-09-12T11:08:18,014 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:18,015 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:18,016 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:18,016 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:18,017 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:18,018 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:18,019 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:18,019 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:18,020 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:18,021 from include/openbabel/mol.h:35: 2023-09-12T11:08:18,021 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:18,022 131 | struct binary_function 2023-09-12T11:08:18,022 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:18,278 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACCARTFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:18,278 ./src/formats/mopacformat.cpp:642:19: warning: variable ‘isotopeMass’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:08:18,279 642 | double x,y,z, isotopeMass; 2023-09-12T11:08:18,280 | ^~~~~~~~~~~ 2023-09-12T11:08:23,237 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:08:23,237 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:08:23,238 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:23,239 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:08:23,239 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:23,298 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:08:23,298 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:24,482 In file included from include/openbabel/atom.h:35: 2023-09-12T11:08:24,482 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2023-09-12T11:08:24,483 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2023-09-12T11:08:24,483 include/openbabel/math/vector3.h:91:11: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:24,484 91 | _vy = inY; 2023-09-12T11:08:24,484 | ~~~~^~~~~ 2023-09-12T11:08:24,485 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:24,485 ./src/formats/mopacformat.cpp:73:14: note: ‘y’ was declared here 2023-09-12T11:08:24,486 73 | double x,y,z; 2023-09-12T11:08:24,487 | ^ 2023-09-12T11:08:24,488 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2023-09-12T11:08:24,488 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2023-09-12T11:08:24,489 include/openbabel/math/vector3.h:90:11: warning: ‘x’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:24,490 90 | _vx = inX; 2023-09-12T11:08:24,491 | ~~~~^~~~~ 2023-09-12T11:08:24,492 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:24,492 ./src/formats/mopacformat.cpp:73:12: note: ‘x’ was declared here 2023-09-12T11:08:24,493 73 | double x,y,z; 2023-09-12T11:08:24,494 | ^ 2023-09-12T11:08:24,538 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,539 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,539 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:283:42: 2023-09-12T11:08:24,540 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,541 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,541 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,542 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,543 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,543 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:309:34: 2023-09-12T11:08:24,544 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,545 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,545 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,546 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,547 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,547 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:331:34: 2023-09-12T11:08:24,548 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,548 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,549 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,549 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,550 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,551 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:377:36: 2023-09-12T11:08:24,551 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,552 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,553 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,554 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,555 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,555 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:396:28: 2023-09-12T11:08:24,556 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,557 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,557 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,558 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,559 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,559 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:402:28: 2023-09-12T11:08:24,560 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,561 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,561 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,562 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,562 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,563 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:409:28: 2023-09-12T11:08:24,564 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,564 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,565 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,565 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:08:24,566 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,566 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:416:59: 2023-09-12T11:08:24,567 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,568 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,568 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:24,569 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:24,570 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:08:24,571 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:433:34: 2023-09-12T11:08:24,572 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:08:24,573 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:24,573 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:27,414 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mopacformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:27,415 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mopacformat.o /tmp/ccHOM5Af.s 2023-09-12T11:08:27,420 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:28,075 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:28,075 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:28,076 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mopacformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mopacformat.' 2023-09-12T11:08:28,079 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mpdformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mpdformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:28,083 Using built-in specs. 2023-09-12T11:08:28,084 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:28,084 Target: arm-linux-gnueabihf 2023-09-12T11:08:28,085 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:28,085 Thread model: posix 2023-09-12T11:08:28,086 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:28,087 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:28,088 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:28,088 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mpdformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mpdformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccLWhjJg.s 2023-09-12T11:08:28,096 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:28,097 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:28,098 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:28,098 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:28,099 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:28,099 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:28,100 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:28,100 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:28,101 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:28,101 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:28,102 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:28,102 #include "..." search starts here: 2023-09-12T11:08:28,102 #include <...> search starts here: 2023-09-12T11:08:28,103 /usr/include/eigen3 2023-09-12T11:08:28,104 include 2023-09-12T11:08:28,104 /usr/include/python3.11 2023-09-12T11:08:28,105 /usr/include/c++/12 2023-09-12T11:08:28,105 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:28,106 /usr/include/c++/12/backward 2023-09-12T11:08:28,107 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:28,107 /usr/local/include 2023-09-12T11:08:28,108 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:28,109 /usr/include 2023-09-12T11:08:28,110 End of search list. 2023-09-12T11:08:28,110 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:28,111 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:28,112 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:28,113 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:28,114 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:29,708 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:29,708 from include/openbabel/mol.h:43, 2023-09-12T11:08:29,709 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:29,710 from ./src/formats/mpdformat.cpp:22: 2023-09-12T11:08:29,710 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:29,711 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:29,712 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:29,713 | ^ 2023-09-12T11:08:29,713 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:29,714 37 | # define UNUSED(x) x 2023-09-12T11:08:29,715 | ^ 2023-09-12T11:08:30,475 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:30,476 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,477 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,478 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:30,478 | ^ 2023-09-12T11:08:30,479 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:30,479 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:30,480 | ^~~~~~~~ 2023-09-12T11:08:30,481 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,481 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,482 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:30,482 | ^ 2023-09-12T11:08:30,483 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:30,484 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:30,484 | ^~~~~~~~ 2023-09-12T11:08:30,499 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,500 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,501 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:30,502 | ^ 2023-09-12T11:08:30,502 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:30,503 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:30,504 | ^~~~~~~~ 2023-09-12T11:08:30,506 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,506 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,507 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:30,508 | ^ 2023-09-12T11:08:30,508 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:30,509 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:30,510 | ^~~~~~~~ 2023-09-12T11:08:30,679 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:30,679 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:30,680 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:30,681 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:30,681 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:30,682 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:30,683 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:30,683 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:30,684 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:30,684 from include/openbabel/mol.h:35: 2023-09-12T11:08:30,685 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:30,685 131 | struct binary_function 2023-09-12T11:08:30,686 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:30,902 ./src/formats/mpdformat.cpp: In member function ‘virtual bool OpenBabel::MPDFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:30,902 ./src/formats/mpdformat.cpp:204:42: warning: variable ‘idx_true’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:08:30,903 204 | bool xml_true=false, pre_true=false, idx_true=false; 2023-09-12T11:08:30,903 | ^~~~~~~~ 2023-09-12T11:08:33,546 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:33,546 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mpdformat.o /tmp/ccLWhjJg.s 2023-09-12T11:08:33,550 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:33,728 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:33,729 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:33,731 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpdformat.' 2023-09-12T11:08:33,731 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/mpqcformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/mpqcformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:33,734 Using built-in specs. 2023-09-12T11:08:33,735 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:33,736 Target: arm-linux-gnueabihf 2023-09-12T11:08:33,736 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:33,737 Thread model: posix 2023-09-12T11:08:33,738 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:33,738 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:33,739 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpqcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:33,739 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mpqcformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase mpqcformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccaV8vKP.s 2023-09-12T11:08:33,747 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:33,748 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:33,749 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:33,750 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:33,750 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:33,751 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:33,751 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:33,752 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:33,752 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:33,753 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:33,754 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:33,754 #include "..." search starts here: 2023-09-12T11:08:33,755 #include <...> search starts here: 2023-09-12T11:08:33,755 /usr/include/eigen3 2023-09-12T11:08:33,756 include 2023-09-12T11:08:33,757 /usr/include/python3.11 2023-09-12T11:08:33,757 /usr/include/c++/12 2023-09-12T11:08:33,758 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:33,758 /usr/include/c++/12/backward 2023-09-12T11:08:33,759 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:33,760 /usr/local/include 2023-09-12T11:08:33,760 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:33,761 /usr/include 2023-09-12T11:08:33,762 End of search list. 2023-09-12T11:08:33,762 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:33,763 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:33,764 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:33,764 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:33,765 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:35,332 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:35,332 from include/openbabel/mol.h:43, 2023-09-12T11:08:35,333 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:35,333 from ./src/formats/mpqcformat.cpp:16: 2023-09-12T11:08:35,334 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:35,334 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:35,335 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:35,335 | ^ 2023-09-12T11:08:35,336 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:35,336 37 | # define UNUSED(x) x 2023-09-12T11:08:35,337 | ^ 2023-09-12T11:08:36,101 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:36,102 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:36,103 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:36,103 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:36,104 | ^ 2023-09-12T11:08:36,105 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:36,105 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:36,106 | ^~~~~~~~ 2023-09-12T11:08:36,107 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:36,107 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:36,108 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:36,108 | ^ 2023-09-12T11:08:36,109 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:36,110 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:36,110 | ^~~~~~~~ 2023-09-12T11:08:36,126 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:36,126 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:36,127 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:36,128 | ^ 2023-09-12T11:08:36,129 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:36,129 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:36,130 | ^~~~~~~~ 2023-09-12T11:08:36,132 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:36,133 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:36,133 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:36,134 | ^ 2023-09-12T11:08:36,134 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:36,135 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:36,135 | ^~~~~~~~ 2023-09-12T11:08:36,305 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:36,306 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:36,306 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:36,307 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:36,308 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:36,308 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:36,309 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:36,310 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:36,310 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:36,311 from include/openbabel/mol.h:35: 2023-09-12T11:08:36,312 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:36,312 131 | struct binary_function 2023-09-12T11:08:36,313 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:38,993 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpqcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:38,994 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/mpqcformat.o /tmp/ccaV8vKP.s 2023-09-12T11:08:39,001 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:39,163 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:39,164 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:39,164 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpqcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/mpqcformat.' 2023-09-12T11:08:39,165 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/msiformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/msiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:39,170 Using built-in specs. 2023-09-12T11:08:39,171 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:39,171 Target: arm-linux-gnueabihf 2023-09-12T11:08:39,171 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:39,172 Thread model: posix 2023-09-12T11:08:39,172 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:39,173 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:39,173 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/msiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:39,174 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/msiformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase msiformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc5SIoI5.s 2023-09-12T11:08:39,183 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:39,183 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:39,185 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:39,185 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:39,186 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:39,187 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:39,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:39,188 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:39,189 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:39,189 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:39,189 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:39,190 #include "..." search starts here: 2023-09-12T11:08:39,190 #include <...> search starts here: 2023-09-12T11:08:39,191 /usr/include/eigen3 2023-09-12T11:08:39,191 include 2023-09-12T11:08:39,191 /usr/include/python3.11 2023-09-12T11:08:39,192 /usr/include/c++/12 2023-09-12T11:08:39,192 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:39,193 /usr/include/c++/12/backward 2023-09-12T11:08:39,193 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:39,194 /usr/local/include 2023-09-12T11:08:39,194 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:39,194 /usr/include 2023-09-12T11:08:39,195 End of search list. 2023-09-12T11:08:39,195 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:39,196 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:39,197 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:39,197 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:39,201 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:40,763 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:40,764 from include/openbabel/mol.h:43, 2023-09-12T11:08:40,764 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:40,765 from ./src/formats/msiformat.cpp:15: 2023-09-12T11:08:40,766 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:40,766 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:40,767 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:40,768 | ^ 2023-09-12T11:08:40,769 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:40,769 37 | # define UNUSED(x) x 2023-09-12T11:08:40,770 | ^ 2023-09-12T11:08:41,532 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:41,532 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:41,533 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:41,534 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:41,534 | ^ 2023-09-12T11:08:41,535 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:41,536 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:41,536 | ^~~~~~~~ 2023-09-12T11:08:41,537 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:41,538 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:41,539 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:41,540 | ^ 2023-09-12T11:08:41,540 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:41,541 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:41,542 | ^~~~~~~~ 2023-09-12T11:08:41,557 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:41,558 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:41,558 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:41,559 | ^ 2023-09-12T11:08:41,559 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:41,560 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:41,561 | ^~~~~~~~ 2023-09-12T11:08:41,565 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:41,565 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:41,566 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:41,566 | ^ 2023-09-12T11:08:41,567 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:41,568 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:41,569 | ^~~~~~~~ 2023-09-12T11:08:41,738 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:41,739 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:41,739 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:41,740 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:41,741 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:41,741 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:41,742 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:41,743 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:41,743 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:41,744 from include/openbabel/mol.h:35: 2023-09-12T11:08:41,745 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:41,745 131 | struct binary_function 2023-09-12T11:08:41,746 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:41,953 ./src/formats/msiformat.cpp: In member function ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:41,954 ./src/formats/msiformat.cpp:71:17: warning: unused variable ‘title’ [-Wunused-variable] 2023-09-12T11:08:41,955 71 | const char* title = pConv->GetTitle(); 2023-09-12T11:08:41,956 | ^~~~~ 2023-09-12T11:08:44,360 In member function ‘void OpenBabel::OBUnitCell::SetSpaceGroup(const OpenBabel::SpaceGroup*)’, 2023-09-12T11:08:44,360 inlined from ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/msiformat.cpp:265:26: 2023-09-12T11:08:44,361 include/openbabel/generic.h:366:60: warning: ‘sg’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:44,361 366 | void SetSpaceGroup(const SpaceGroup* sg) { _spaceGroup = sg; } 2023-09-12T11:08:44,362 | ~~~~~~~~~~~~^~~~ 2023-09-12T11:08:44,362 ./src/formats/msiformat.cpp: In member function ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:44,363 ./src/formats/msiformat.cpp:106:23: note: ‘sg’ was declared here 2023-09-12T11:08:44,364 106 | const SpaceGroup *sg; 2023-09-12T11:08:44,364 | ^~ 2023-09-12T11:08:44,365 ./src/formats/msiformat.cpp:189:28: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:44,365 189 | atom->SetVector(atof(vs[3].c_str()), 2023-09-12T11:08:44,366 | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:44,367 190 | atof(vs[4].c_str()), 2023-09-12T11:08:44,367 | ~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:44,368 191 | atof(vs[5].c_str())); 2023-09-12T11:08:44,368 | ~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:44,369 ./src/formats/msiformat.cpp:103:13: note: ‘atom’ was declared here 2023-09-12T11:08:44,370 103 | OBAtom *atom; 2023-09-12T11:08:44,371 | ^~~~ 2023-09-12T11:08:44,371 ./src/formats/msiformat.cpp:235:24: warning: ‘bondOrder’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:44,372 235 | mol.AddBond(startBondAtom - 1, endBondAtom - 1, bondOrder); 2023-09-12T11:08:44,373 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:44,374 ./src/formats/msiformat.cpp:100:46: note: ‘bondOrder’ was declared here 2023-09-12T11:08:44,374 100 | unsigned int startBondAtom, endBondAtom, bondOrder; 2023-09-12T11:08:44,375 | ^~~~~~~~~ 2023-09-12T11:08:44,376 ./src/formats/msiformat.cpp:235:56: warning: ‘endBondAtom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:44,377 235 | mol.AddBond(startBondAtom - 1, endBondAtom - 1, bondOrder); 2023-09-12T11:08:44,377 | ~~~~~~~~~~~~^~~ 2023-09-12T11:08:44,378 ./src/formats/msiformat.cpp:100:33: note: ‘endBondAtom’ was declared here 2023-09-12T11:08:44,378 100 | unsigned int startBondAtom, endBondAtom, bondOrder; 2023-09-12T11:08:44,379 | ^~~~~~~~~~~ 2023-09-12T11:08:44,380 ./src/formats/msiformat.cpp:235:39: warning: ‘startBondAtom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:44,380 235 | mol.AddBond(startBondAtom - 1, endBondAtom - 1, bondOrder); 2023-09-12T11:08:44,381 | ~~~~~~~~~~~~~~^~~ 2023-09-12T11:08:44,382 ./src/formats/msiformat.cpp:100:18: note: ‘startBondAtom’ was declared here 2023-09-12T11:08:44,382 100 | unsigned int startBondAtom, endBondAtom, bondOrder; 2023-09-12T11:08:44,383 | ^~~~~~~~~~~~~ 2023-09-12T11:08:45,364 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/msiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:45,365 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/msiformat.o /tmp/cc5SIoI5.s 2023-09-12T11:08:45,371 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:45,590 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:45,591 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:45,592 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/msiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/msiformat.' 2023-09-12T11:08:45,593 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/msmsformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/msmsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:45,599 Using built-in specs. 2023-09-12T11:08:45,601 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:45,602 Target: arm-linux-gnueabihf 2023-09-12T11:08:45,602 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:45,603 Thread model: posix 2023-09-12T11:08:45,604 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:45,604 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:45,605 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/msmsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:45,606 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/msmsformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase msmsformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccgSnNsl.s 2023-09-12T11:08:45,618 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:45,619 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:45,620 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:45,620 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:45,621 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:45,622 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:45,622 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:45,623 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:45,623 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:45,624 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:45,624 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:45,625 #include "..." search starts here: 2023-09-12T11:08:45,626 #include <...> search starts here: 2023-09-12T11:08:45,626 /usr/include/eigen3 2023-09-12T11:08:45,627 include 2023-09-12T11:08:45,628 /usr/include/python3.11 2023-09-12T11:08:45,629 /usr/include/c++/12 2023-09-12T11:08:45,629 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:45,630 /usr/include/c++/12/backward 2023-09-12T11:08:45,631 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:45,631 /usr/local/include 2023-09-12T11:08:45,632 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:45,633 /usr/include 2023-09-12T11:08:45,634 End of search list. 2023-09-12T11:08:45,634 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:45,635 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:45,636 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:45,637 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:45,644 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:47,228 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:47,229 from include/openbabel/mol.h:43, 2023-09-12T11:08:47,230 from ./src/formats/msmsformat.cpp:26: 2023-09-12T11:08:47,230 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:47,231 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:47,232 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:47,232 | ^ 2023-09-12T11:08:47,233 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:47,234 37 | # define UNUSED(x) x 2023-09-12T11:08:47,234 | ^ 2023-09-12T11:08:47,997 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:47,997 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:47,998 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:47,999 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:48,000 | ^ 2023-09-12T11:08:48,000 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:48,001 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:48,001 | ^~~~~~~~ 2023-09-12T11:08:48,002 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:48,003 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:48,003 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:48,004 | ^ 2023-09-12T11:08:48,004 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:48,005 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:48,006 | ^~~~~~~~ 2023-09-12T11:08:48,021 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:48,022 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:48,022 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:48,023 | ^ 2023-09-12T11:08:48,024 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:48,024 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:48,025 | ^~~~~~~~ 2023-09-12T11:08:48,027 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:48,028 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:48,029 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:48,029 | ^ 2023-09-12T11:08:48,030 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:48,031 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:48,031 | ^~~~~~~~ 2023-09-12T11:08:48,201 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:48,201 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:48,202 from ./src/formats/msmsformat.cpp:27: 2023-09-12T11:08:48,203 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:48,204 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:48,205 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:48,205 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:48,206 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:48,206 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:48,207 from include/openbabel/mol.h:35: 2023-09-12T11:08:48,207 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:48,208 131 | struct binary_function 2023-09-12T11:08:48,208 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:48,400 ./src/formats/msmsformat.cpp: In member function ‘virtual int OpenBabel::OBMSMSFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:08:48,400 ./src/formats/msmsformat.cpp:82:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:08:48,401 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:08:48,402 | ~~~~^ 2023-09-12T11:08:48,402 ./src/formats/msmsformat.cpp:82:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:08:48,403 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:08:48,403 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:08:50,566 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/msmsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:50,566 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/msmsformat.o /tmp/ccgSnNsl.s 2023-09-12T11:08:50,571 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:50,704 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:50,705 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:50,705 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/msmsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/msmsformat.' 2023-09-12T11:08:50,706 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/nulformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/nulformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:50,710 Using built-in specs. 2023-09-12T11:08:50,711 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:50,712 Target: arm-linux-gnueabihf 2023-09-12T11:08:50,712 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:50,713 Thread model: posix 2023-09-12T11:08:50,713 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:50,714 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:50,714 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/nulformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:50,715 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/nulformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase nulformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cctHC9BB.s 2023-09-12T11:08:50,724 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:50,725 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:50,726 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:50,726 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:50,727 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:50,727 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:50,728 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:50,728 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:50,729 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:50,730 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:50,730 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:50,731 #include "..." search starts here: 2023-09-12T11:08:50,731 #include <...> search starts here: 2023-09-12T11:08:50,732 /usr/include/eigen3 2023-09-12T11:08:50,732 include 2023-09-12T11:08:50,733 /usr/include/python3.11 2023-09-12T11:08:50,734 /usr/include/c++/12 2023-09-12T11:08:50,734 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:50,735 /usr/include/c++/12/backward 2023-09-12T11:08:50,736 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:50,736 /usr/local/include 2023-09-12T11:08:50,737 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:50,737 /usr/include 2023-09-12T11:08:50,738 End of search list. 2023-09-12T11:08:50,738 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:50,739 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:50,740 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:50,740 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:50,744 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:52,179 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:52,180 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:52,180 from ./src/formats/nulformat.cpp:14: 2023-09-12T11:08:52,181 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:52,182 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:52,182 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:52,183 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:08:52,184 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:08:52,184 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:08:52,185 from /usr/include/c++/12/ios:42, 2023-09-12T11:08:52,185 from /usr/include/c++/12/ostream:38, 2023-09-12T11:08:52,186 from /usr/include/c++/12/iostream:39, 2023-09-12T11:08:52,186 from include/openbabel/obconversion.h:24: 2023-09-12T11:08:52,187 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:52,188 131 | struct binary_function 2023-09-12T11:08:52,188 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:52,328 In file included from ./src/formats/nulformat.cpp:15: 2023-09-12T11:08:52,329 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:52,329 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:52,330 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:52,331 | ^ 2023-09-12T11:08:52,331 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:52,332 37 | # define UNUSED(x) x 2023-09-12T11:08:52,333 | ^ 2023-09-12T11:08:53,195 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/nulformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:53,195 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/nulformat.o /tmp/cctHC9BB.s 2023-09-12T11:08:53,200 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:53,279 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:08:53,279 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:08:53,280 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/nulformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/nulformat.' 2023-09-12T11:08:53,280 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/nwchemformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/nwchemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:53,284 Using built-in specs. 2023-09-12T11:08:53,285 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:53,286 Target: arm-linux-gnueabihf 2023-09-12T11:08:53,286 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:08:53,287 Thread model: posix 2023-09-12T11:08:53,287 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:53,288 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:53,288 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/nwchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:08:53,289 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/nwchemformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase nwchemformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc4hNY4k.s 2023-09-12T11:08:53,297 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:53,298 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:53,299 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:53,300 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:53,300 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:53,300 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:53,301 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:53,301 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:53,302 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:53,302 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:53,303 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:53,303 #include "..." search starts here: 2023-09-12T11:08:53,304 #include <...> search starts here: 2023-09-12T11:08:53,304 /usr/include/eigen3 2023-09-12T11:08:53,304 include 2023-09-12T11:08:53,305 /usr/include/python3.11 2023-09-12T11:08:53,305 /usr/include/c++/12 2023-09-12T11:08:53,306 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:53,306 /usr/include/c++/12/backward 2023-09-12T11:08:53,307 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:53,307 /usr/local/include 2023-09-12T11:08:53,308 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:53,308 /usr/include 2023-09-12T11:08:53,309 End of search list. 2023-09-12T11:08:53,309 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:53,310 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:53,311 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:53,312 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:53,317 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:55,113 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:55,114 from include/openbabel/mol.h:43, 2023-09-12T11:08:55,114 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:55,115 from ./src/formats/nwchemformat.cpp:17: 2023-09-12T11:08:55,116 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:55,117 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:55,117 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:55,118 | ^ 2023-09-12T11:08:55,118 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:55,119 37 | # define UNUSED(x) x 2023-09-12T11:08:55,120 | ^ 2023-09-12T11:08:55,890 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:55,891 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:55,891 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:55,892 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:55,892 | ^ 2023-09-12T11:08:55,893 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:55,894 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:55,895 | ^~~~~~~~ 2023-09-12T11:08:55,897 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:55,897 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:55,898 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:55,898 | ^ 2023-09-12T11:08:55,899 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:55,900 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:55,900 | ^~~~~~~~ 2023-09-12T11:08:55,917 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:55,918 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:55,918 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:55,919 | ^ 2023-09-12T11:08:55,919 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:55,920 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:55,921 | ^~~~~~~~ 2023-09-12T11:08:55,925 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:55,925 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:55,926 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:55,927 | ^ 2023-09-12T11:08:55,927 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:55,928 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:55,929 | ^~~~~~~~ 2023-09-12T11:08:56,099 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:56,099 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:56,100 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:56,101 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:56,101 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:56,102 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:56,103 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:56,103 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:56,104 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:56,105 from include/openbabel/mol.h:35: 2023-09-12T11:08:56,106 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:56,106 131 | struct binary_function 2023-09-12T11:08:56,107 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:56,311 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:08:56,311 ./src/formats/nwchemformat.cpp:221:72: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:08:56,312 221 | if ((i>=natoms) || (molecule->GetAtom(i+1)->GetAtomicNum() != atoi(vs[2].c_str()))) 2023-09-12T11:08:56,312 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:56,318 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMultipoleMoment(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:08:56,318 ./src/formats/nwchemformat.cpp:296:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2023-09-12T11:08:56,319 296 | else if (vs[0][0] == '1') 2023-09-12T11:08:56,319 | ^ 2023-09-12T11:08:56,324 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadPartialCharges(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:08:56,325 ./src/formats/nwchemformat.cpp:413:56: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:08:56,325 413 | if (molecule->GetAtom(i++)->GetAtomicNum() != charge) 2023-09-12T11:08:56,326 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:08:56,335 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMEPCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:08:56,336 ./src/formats/nwchemformat.cpp:561:25: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:08:56,337 561 | if (energies.size() != molecule->NumConformers()) 2023-09-12T11:08:56,338 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:56,379 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadNEBCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:08:56,380 ./src/formats/nwchemformat.cpp:826:79: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:08:56,380 826 | if (etab.GetAtomicNum(vs[1].substr(0, end_of_symbol).c_str()) != molecule->GetAtom(i+1)->GetAtomicNum()) 2023-09-12T11:08:56,381 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:56,389 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:08:56,389 ./src/formats/nwchemformat.cpp:914:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:08:56,390 914 | if (atoi(buffer) != natoms) 2023-09-12T11:08:56,391 | ~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:08:56,391 ./src/formats/nwchemformat.cpp:924:84: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:08:56,392 924 | if ((vs.size() < 4) || (molecule->GetAtom(i+1)->GetAtomicNum() != etab.GetAtomicNum(vs[0].c_str()))) 2023-09-12T11:08:56,393 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:57,834 ./src/formats/nwchemformat.cpp: At global scope: 2023-09-12T11:08:57,835 ./src/formats/nwchemformat.cpp:104:20: warning: ‘OpenBabel::BETA_ORBITAL_PATTERN’ defined but not used [-Wunused-variable] 2023-09-12T11:08:57,835 104 | static const char* BETA_ORBITAL_PATTERN = "Beta"; 2023-09-12T11:08:57,836 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:00,503 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:09:00,503 ./src/formats/nwchemformat.cpp:237:18: warning: ‘coordinates’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:09:00,504 237 | delete[] coordinates; 2023-09-12T11:09:00,504 | ^~~~~~~~~~~ 2023-09-12T11:09:00,505 ./src/formats/nwchemformat.cpp:195:13: note: ‘coordinates’ was declared here 2023-09-12T11:09:00,506 195 | double* coordinates; 2023-09-12T11:09:00,506 | ^~~~~~~~~~~ 2023-09-12T11:09:01,250 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:09:01,251 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:09:01,252 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:01,252 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:09:01,255 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:01,457 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:09:01,458 ./src/formats/nwchemformat.cpp:939:21: warning: ‘nbeads’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:09:01,459 939 | if (bead_number != nbeads) 2023-09-12T11:09:01,459 | ^~ 2023-09-12T11:09:01,460 ./src/formats/nwchemformat.cpp:886:18: note: ‘nbeads’ was declared here 2023-09-12T11:09:01,461 886 | unsigned int nbeads; 2023-09-12T11:09:01,462 | ^~~~~~ 2023-09-12T11:09:01,468 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:09:01,468 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:01,469 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:933:35: 2023-09-12T11:09:01,470 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:01,471 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:09:01,471 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:09:01,742 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:09:01,742 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:01,743 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:09:01,744 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:01,875 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:01,876 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:01,877 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadPartialCharges(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:418:34: 2023-09-12T11:09:01,877 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:01,878 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:01,879 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:02,130 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:02,131 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:02,132 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadMEPCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:550:43: 2023-09-12T11:09:02,132 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:02,133 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:02,133 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:02,375 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:02,376 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:02,377 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadTDDFTCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:346:34: 2023-09-12T11:09:02,377 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:02,378 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:02,379 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:02,380 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:02,380 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:02,381 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadTDDFTCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:351:46: 2023-09-12T11:09:02,382 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:02,383 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:02,383 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:02,384 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:02,384 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:02,385 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadTDDFTCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:359:46: 2023-09-12T11:09:02,386 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:02,386 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:02,387 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:02,691 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:09:02,691 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:02,692 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:09:02,692 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:02,932 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:02,933 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:02,933 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadNEBCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:851:35: 2023-09-12T11:09:02,934 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:02,934 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:02,935 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:03,724 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBOrbital&}; _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’: 2023-09-12T11:09:03,725 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:03,726 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:09:03,727 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:03,832 In file included from /usr/include/c++/12/vector:63: 2023-09-12T11:09:03,832 /usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’: 2023-09-12T11:09:03,833 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:03,834 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2023-09-12T11:09:03,835 | ^~~~~~~~~~~~~~~~ 2023-09-12T11:09:03,835 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:03,923 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:03,924 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:03,925 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:03,926 inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35, 2023-09-12T11:09:03,926 inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/vector.tcc:232:44: 2023-09-12T11:09:03,927 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:03,927 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:03,927 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:04,038 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:04,039 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:04,040 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:04,040 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:04,041 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:09:04,042 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:09:04,042 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:04,043 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:04,043 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:04,044 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:04,045 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:04,046 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:04,046 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:04,047 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:09:04,047 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:09:04,048 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:04,048 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:04,049 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:04,380 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’, 2023-09-12T11:09:04,381 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:482:31: 2023-09-12T11:09:04,382 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:04,382 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:09:04,383 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:09:04,384 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:04,385 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:04,386 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:04,386 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:04,387 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:493:43: 2023-09-12T11:09:04,388 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:04,389 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:04,389 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:04,390 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:04,390 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:04,391 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:04,391 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:04,392 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:502:46: 2023-09-12T11:09:04,393 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:04,394 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:04,395 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:04,395 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:04,396 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:04,397 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:04,398 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:04,398 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:504:47: 2023-09-12T11:09:04,399 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:04,400 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:04,401 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:04,974 In member function ‘void OpenBabel::OBMol::SetEnergy(double)’, 2023-09-12T11:09:04,974 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadSinglePointCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:760:24: 2023-09-12T11:09:04,975 include/openbabel/mol.h:418:47: warning: ‘energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:09:04,975 418 | void SetEnergy(double energy) { _energy = energy; } 2023-09-12T11:09:04,976 | ~~~~~~~~^~~~~~~~ 2023-09-12T11:09:04,977 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadSinglePointCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:09:04,977 ./src/formats/nwchemformat.cpp:736:12: note: ‘energy’ was declared here 2023-09-12T11:09:04,978 736 | double energy; 2023-09-12T11:09:04,978 | ^~~~~~ 2023-09-12T11:09:05,152 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:05,152 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:05,153 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadGeometryOptimizationCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:606:35: 2023-09-12T11:09:05,154 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,154 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:05,155 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:05,636 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:05,637 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:05,638 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:658:31: 2023-09-12T11:09:05,638 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,639 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:05,640 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:05,640 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:05,641 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:05,642 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:666:32: 2023-09-12T11:09:05,642 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,643 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:05,644 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:05,645 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:05,645 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:05,646 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:670:32: 2023-09-12T11:09:05,646 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,647 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:05,647 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:05,648 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:05,648 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:05,649 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:674:32: 2023-09-12T11:09:05,649 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,650 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:05,651 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:05,652 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:09:05,653 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:05,653 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:683:37: 2023-09-12T11:09:05,654 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,655 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:05,656 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:05,656 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:05,657 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:689:36: 2023-09-12T11:09:05,658 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,658 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:09:05,659 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:09:05,660 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:05,661 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:05,662 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:702:42: 2023-09-12T11:09:05,662 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:05,663 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:05,663 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:06,829 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/nwchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:06,830 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/nwchemformat.o /tmp/cc4hNY4k.s 2023-09-12T11:09:06,834 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:07,685 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:09:07,686 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:09:07,686 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/nwchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/nwchemformat.' 2023-09-12T11:09:07,690 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/opendxformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/opendxformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:09:07,694 Using built-in specs. 2023-09-12T11:09:07,695 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:07,695 Target: arm-linux-gnueabihf 2023-09-12T11:09:07,696 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:09:07,696 Thread model: posix 2023-09-12T11:09:07,697 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:07,698 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:07,698 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/opendxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:07,698 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/opendxformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase opendxformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc8uyHm3.s 2023-09-12T11:09:07,708 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:07,708 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:07,709 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:07,710 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:07,711 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:07,711 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:07,712 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:07,713 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:07,713 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:07,714 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:07,714 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:07,715 #include "..." search starts here: 2023-09-12T11:09:07,716 #include <...> search starts here: 2023-09-12T11:09:07,716 /usr/include/eigen3 2023-09-12T11:09:07,717 include 2023-09-12T11:09:07,718 /usr/include/python3.11 2023-09-12T11:09:07,718 /usr/include/c++/12 2023-09-12T11:09:07,719 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:07,719 /usr/include/c++/12/backward 2023-09-12T11:09:07,720 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:07,720 /usr/local/include 2023-09-12T11:09:07,721 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:07,722 /usr/include 2023-09-12T11:09:07,722 End of search list. 2023-09-12T11:09:07,723 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:07,723 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:07,725 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:07,725 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:07,726 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:09,280 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:09,281 from include/openbabel/mol.h:43, 2023-09-12T11:09:09,282 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:09,282 from ./src/formats/opendxformat.cpp:24: 2023-09-12T11:09:09,283 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:09,283 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:09,284 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:09,284 | ^ 2023-09-12T11:09:09,285 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:09,285 37 | # define UNUSED(x) x 2023-09-12T11:09:09,286 | ^ 2023-09-12T11:09:10,051 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:10,051 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:10,052 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:10,053 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:10,053 | ^ 2023-09-12T11:09:10,054 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:10,055 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:10,056 | ^~~~~~~~ 2023-09-12T11:09:10,057 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:10,057 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:10,058 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:10,059 | ^ 2023-09-12T11:09:10,060 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:10,060 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:10,061 | ^~~~~~~~ 2023-09-12T11:09:10,075 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:10,076 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:10,077 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:10,077 | ^ 2023-09-12T11:09:10,078 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:10,079 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:10,080 | ^~~~~~~~ 2023-09-12T11:09:10,082 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:10,082 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:10,084 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:10,084 | ^ 2023-09-12T11:09:10,085 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:10,085 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:10,086 | ^~~~~~~~ 2023-09-12T11:09:10,255 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:10,256 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:10,256 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:10,257 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:10,258 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:10,259 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:10,259 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:10,260 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:09:10,261 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:09:10,261 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:09:10,262 from /usr/include/c++/12/ios:42, 2023-09-12T11:09:10,263 from /usr/include/c++/12/istream:38, 2023-09-12T11:09:10,263 from /usr/include/c++/12/sstream:38, 2023-09-12T11:09:10,264 from ./src/formats/opendxformat.cpp:21: 2023-09-12T11:09:10,265 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:10,265 131 | struct binary_function 2023-09-12T11:09:10,266 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:10,457 ./src/formats/opendxformat.cpp: In member function ‘virtual int OpenBabel::OBOpenDXCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:09:10,458 ./src/formats/opendxformat.cpp:65:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:09:10,459 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:09:10,460 | ~~~~^ 2023-09-12T11:09:10,460 ./src/formats/opendxformat.cpp:65:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:09:10,461 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:09:10,462 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:09:13,364 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:09:13,365 from include/openbabel/mol.h:35: 2023-09-12T11:09:13,365 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:09:13,366 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:13,367 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:09:13,368 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:13,426 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:09:13,427 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:13,651 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:09:13,652 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:13,653 inlined from ‘virtual bool OpenBabel::OBOpenDXCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/opendxformat.cpp:149:23: 2023-09-12T11:09:13,653 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:13,654 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:13,654 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:13,655 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:13,655 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:13,656 inlined from ‘virtual bool OpenBabel::OBOpenDXCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/opendxformat.cpp:194:25: 2023-09-12T11:09:13,657 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:13,658 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:13,658 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:14,314 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/opendxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:14,315 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/opendxformat.o /tmp/cc8uyHm3.s 2023-09-12T11:09:14,319 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:14,587 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:09:14,587 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:09:14,588 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/opendxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/opendxformat.' 2023-09-12T11:09:14,589 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/orcaformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/orcaformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:09:14,593 Using built-in specs. 2023-09-12T11:09:14,594 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:14,595 Target: arm-linux-gnueabihf 2023-09-12T11:09:14,595 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:09:14,596 Thread model: posix 2023-09-12T11:09:14,596 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:14,597 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:14,598 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/orcaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:14,598 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/orcaformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase orcaformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc92kMo3.s 2023-09-12T11:09:14,607 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:14,608 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:14,609 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:14,610 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:14,610 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:14,611 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:14,612 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:14,612 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:14,613 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:14,613 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:14,614 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:14,614 #include "..." search starts here: 2023-09-12T11:09:14,614 #include <...> search starts here: 2023-09-12T11:09:14,615 /usr/include/eigen3 2023-09-12T11:09:14,615 include 2023-09-12T11:09:14,616 /usr/include/python3.11 2023-09-12T11:09:14,616 /usr/include/c++/12 2023-09-12T11:09:14,616 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:14,617 /usr/include/c++/12/backward 2023-09-12T11:09:14,617 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:14,618 /usr/local/include 2023-09-12T11:09:14,618 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:14,618 /usr/include 2023-09-12T11:09:14,619 End of search list. 2023-09-12T11:09:14,619 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:14,620 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:14,620 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:14,621 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:14,632 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:16,241 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:16,242 from include/openbabel/mol.h:43, 2023-09-12T11:09:16,242 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:16,243 from ./src/formats/orcaformat.cpp:18: 2023-09-12T11:09:16,244 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:16,244 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:16,245 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:16,246 | ^ 2023-09-12T11:09:16,246 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:16,247 37 | # define UNUSED(x) x 2023-09-12T11:09:16,248 | ^ 2023-09-12T11:09:17,014 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:17,014 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,015 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,015 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:17,016 | ^ 2023-09-12T11:09:17,017 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:17,017 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:17,018 | ^~~~~~~~ 2023-09-12T11:09:17,022 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,022 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,023 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:17,024 | ^ 2023-09-12T11:09:17,025 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:17,025 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:17,026 | ^~~~~~~~ 2023-09-12T11:09:17,043 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,044 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,045 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:17,045 | ^ 2023-09-12T11:09:17,046 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:17,047 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:17,047 | ^~~~~~~~ 2023-09-12T11:09:17,052 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,053 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,053 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:17,054 | ^ 2023-09-12T11:09:17,055 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:17,055 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:17,056 | ^~~~~~~~ 2023-09-12T11:09:17,227 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:17,228 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:17,228 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:17,229 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:17,230 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:17,230 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:17,231 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:17,231 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:17,232 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:17,232 from include/openbabel/mol.h:35: 2023-09-12T11:09:17,233 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:17,233 131 | struct binary_function 2023-09-12T11:09:17,234 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:17,609 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:17,610 ./src/formats/orcaformat.cpp:338:33: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:09:17,611 338 | while(vs.size() == nColumn+1) { 2023-09-12T11:09:17,612 | ~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:09:17,614 ./src/formats/orcaformat.cpp:353:48: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:09:17,615 353 | for (unsigned int i = 0; i < nColumn; i++) { 2023-09-12T11:09:17,615 | ~~^~~~~~~~~ 2023-09-12T11:09:17,617 ./src/formats/orcaformat.cpp:365:44: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:09:17,617 365 | for (unsigned int i = 0; i < nColumn; i++) { 2023-09-12T11:09:17,618 | ~~^~~~~~~~~ 2023-09-12T11:09:17,634 ./src/formats/orcaformat.cpp:121:12: warning: unused variable ‘energy’ [-Wunused-variable] 2023-09-12T11:09:17,634 121 | double energy=0; 2023-09-12T11:09:17,635 | ^~~~~~ 2023-09-12T11:09:17,635 ./src/formats/orcaformat.cpp:128:9: warning: variable ‘nModeAll’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:09:17,636 128 | int nModeAll = 0; 2023-09-12T11:09:17,636 | ^~~~~~~~ 2023-09-12T11:09:17,654 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:17,655 ./src/formats/orcaformat.cpp:646:10: warning: unused variable ‘buffer’ [-Wunused-variable] 2023-09-12T11:09:17,655 646 | char buffer[BUFF_SIZE]; 2023-09-12T11:09:17,656 | ^~~~~~ 2023-09-12T11:09:21,851 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:09:21,852 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:09:21,852 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:21,853 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:09:21,854 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:21,913 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:09:21,914 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:22,424 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBOrbital&}; _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’: 2023-09-12T11:09:22,424 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:22,531 In file included from /usr/include/c++/12/vector:63: 2023-09-12T11:09:22,532 /usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’: 2023-09-12T11:09:22,533 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:22,533 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2023-09-12T11:09:22,534 | ^~~~~~~~~~~~~~~~ 2023-09-12T11:09:22,535 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:22,571 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:22,571 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:22,572 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:22,572 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31: 2023-09-12T11:09:22,573 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:22,573 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:22,574 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:22,654 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:22,655 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:22,655 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:22,656 inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35, 2023-09-12T11:09:22,657 inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/vector.tcc:232:44: 2023-09-12T11:09:22,657 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:22,658 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:22,659 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:22,770 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:22,771 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:22,771 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:22,772 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:22,772 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:09:22,773 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:09:22,774 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:22,775 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:22,775 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:22,776 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:22,777 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:22,777 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:22,778 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:22,779 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:09:22,779 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:09:22,780 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:22,781 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:22,781 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,351 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:26,351 ./src/formats/orcaformat.cpp:210:36: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:09:26,352 210 | atom->SetVector(x,y,z); //set atom coordinates 2023-09-12T11:09:26,352 | ~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:09:26,353 ./src/formats/orcaformat.cpp:152:13: note: ‘atom’ was declared here 2023-09-12T11:09:26,353 152 | OBAtom *atom; 2023-09-12T11:09:26,354 | ^~~~ 2023-09-12T11:09:26,354 ./src/formats/orcaformat.cpp:207:37: warning: ‘confCoords’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:09:26,355 207 | confCoords[i*3+2] = z; 2023-09-12T11:09:26,355 | ^ 2023-09-12T11:09:26,356 ./src/formats/orcaformat.cpp:139:13: note: ‘confCoords’ was declared here 2023-09-12T11:09:26,357 139 | double* confCoords; 2023-09-12T11:09:26,357 | ^~~~~~~~~~ 2023-09-12T11:09:26,430 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,431 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,431 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:242:30: 2023-09-12T11:09:26,432 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,432 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,433 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,434 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,434 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,435 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:243:35: 2023-09-12T11:09:26,436 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,436 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,437 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,437 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,438 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,439 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:244:35: 2023-09-12T11:09:26,439 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,440 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,440 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,441 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,441 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,442 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:259:35: 2023-09-12T11:09:26,442 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,443 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,443 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,444 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,444 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,445 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:260:40: 2023-09-12T11:09:26,445 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,446 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,447 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,448 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,448 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,449 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:261:40: 2023-09-12T11:09:26,449 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,450 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,451 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,451 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,452 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,453 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:314:41: 2023-09-12T11:09:26,453 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,454 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,455 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,458 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,459 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,459 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:341:36: 2023-09-12T11:09:26,460 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,460 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,461 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,463 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,464 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,465 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:346:36: 2023-09-12T11:09:26,465 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,466 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,467 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,469 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,470 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,471 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:351:36: 2023-09-12T11:09:26,471 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,472 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,473 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,474 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:09:26,475 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,476 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:355:41: 2023-09-12T11:09:26,476 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,477 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,478 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,483 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,484 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,484 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:392:38: 2023-09-12T11:09:26,485 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,485 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,486 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,486 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,487 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,487 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:393:38: 2023-09-12T11:09:26,488 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,488 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,489 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,491 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,492 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,492 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:410:42: 2023-09-12T11:09:26,493 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,494 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,494 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,497 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,497 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,498 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:430:35: 2023-09-12T11:09:26,498 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,499 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,500 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,501 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,501 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,501 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:431:39: 2023-09-12T11:09:26,502 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,502 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,503 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,503 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,504 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,504 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:432:36: 2023-09-12T11:09:26,505 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,505 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,506 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,508 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,508 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,509 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:451:35: 2023-09-12T11:09:26,510 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,511 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,511 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,512 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,513 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,513 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:452:39: 2023-09-12T11:09:26,514 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,514 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,515 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,516 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,517 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,517 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:453:36: 2023-09-12T11:09:26,518 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,518 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,519 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,520 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,521 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,521 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:473:37: 2023-09-12T11:09:26,521 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,522 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,523 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,523 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,524 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,525 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:474:39: 2023-09-12T11:09:26,525 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,526 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,527 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,527 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:09:26,528 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,529 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:475:44: 2023-09-12T11:09:26,529 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,530 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,530 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,531 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:09:26,532 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:09:26,532 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:492:42: 2023-09-12T11:09:26,533 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,533 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:26,534 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,540 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:09:26,541 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’, 2023-09-12T11:09:26,542 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:559:36: 2023-09-12T11:09:26,542 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,543 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:09:26,543 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:09:26,544 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; bool _TrivialValueTypes = false]’, 2023-09-12T11:09:26,545 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, 2023-09-12T11:09:26,545 inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*; _Tp = OpenBabel::OBOrbital]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, 2023-09-12T11:09:26,546 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, 2023-09-12T11:09:26,547 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:561:30: 2023-09-12T11:09:26,547 /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,548 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:09:26,549 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:26,549 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’, 2023-09-12T11:09:26,550 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:570:39: 2023-09-12T11:09:26,551 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:09:26,552 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:09:26,553 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:09:30,850 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/orcaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:30,851 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/orcaformat.o /tmp/cc92kMo3.s 2023-09-12T11:09:30,856 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:31,635 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:09:31,636 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:09:31,636 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/orcaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/orcaformat.' 2023-09-12T11:09:31,639 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/outformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/outformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:09:31,643 Using built-in specs. 2023-09-12T11:09:31,644 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:31,644 Target: arm-linux-gnueabihf 2023-09-12T11:09:31,645 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:09:31,645 Thread model: posix 2023-09-12T11:09:31,646 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:31,647 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:31,647 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/outformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:31,647 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/outformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase outformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccgRRkAF.s 2023-09-12T11:09:31,656 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:31,656 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:31,657 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:31,658 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:31,659 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:31,659 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:31,660 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:31,661 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:31,661 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:31,662 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:31,663 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:31,663 #include "..." search starts here: 2023-09-12T11:09:31,664 #include <...> search starts here: 2023-09-12T11:09:31,664 /usr/include/eigen3 2023-09-12T11:09:31,665 include 2023-09-12T11:09:31,666 /usr/include/python3.11 2023-09-12T11:09:31,666 /usr/include/c++/12 2023-09-12T11:09:31,667 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:31,667 /usr/include/c++/12/backward 2023-09-12T11:09:31,668 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:31,669 /usr/local/include 2023-09-12T11:09:31,669 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:31,670 /usr/include 2023-09-12T11:09:31,670 End of search list. 2023-09-12T11:09:31,671 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:31,671 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:31,672 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:31,673 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:31,674 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:33,275 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:33,276 from include/openbabel/mol.h:43, 2023-09-12T11:09:33,277 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:33,278 from ./src/formats/outformat.cpp:16: 2023-09-12T11:09:33,278 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:33,279 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:33,280 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:33,280 | ^ 2023-09-12T11:09:33,281 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:33,281 37 | # define UNUSED(x) x 2023-09-12T11:09:33,282 | ^ 2023-09-12T11:09:34,046 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:34,047 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:34,048 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:34,048 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:34,049 | ^ 2023-09-12T11:09:34,049 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:34,050 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:34,050 | ^~~~~~~~ 2023-09-12T11:09:34,052 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:34,052 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:34,053 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:34,054 | ^ 2023-09-12T11:09:34,055 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:34,055 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:34,056 | ^~~~~~~~ 2023-09-12T11:09:34,071 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:34,071 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:34,072 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:34,073 | ^ 2023-09-12T11:09:34,073 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:34,074 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:34,075 | ^~~~~~~~ 2023-09-12T11:09:34,077 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:34,078 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:34,079 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:34,079 | ^ 2023-09-12T11:09:34,080 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:34,081 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:34,081 | ^~~~~~~~ 2023-09-12T11:09:34,251 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:34,252 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:34,252 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:34,253 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:34,253 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:34,254 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:34,255 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:34,255 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:34,256 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:34,256 from include/openbabel/mol.h:35: 2023-09-12T11:09:34,257 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:34,257 131 | struct binary_function 2023-09-12T11:09:34,258 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:36,990 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/outformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:36,990 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/outformat.o /tmp/ccgRRkAF.s 2023-09-12T11:09:36,995 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:37,164 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:09:37,165 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:09:37,166 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/outformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/outformat.' 2023-09-12T11:09:37,166 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/painterformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/painterformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:09:37,171 Using built-in specs. 2023-09-12T11:09:37,172 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:37,172 Target: arm-linux-gnueabihf 2023-09-12T11:09:37,172 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:09:37,173 Thread model: posix 2023-09-12T11:09:37,173 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:37,174 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:37,175 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/painterformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:37,175 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/painterformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase painterformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cch9mnC6.s 2023-09-12T11:09:37,184 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:37,184 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:37,185 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:37,186 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:37,186 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:37,187 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:37,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:37,188 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:37,188 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:37,189 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:37,189 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:37,190 #include "..." search starts here: 2023-09-12T11:09:37,190 #include <...> search starts here: 2023-09-12T11:09:37,191 /usr/include/eigen3 2023-09-12T11:09:37,191 include 2023-09-12T11:09:37,192 /usr/include/python3.11 2023-09-12T11:09:37,192 /usr/include/c++/12 2023-09-12T11:09:37,193 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:37,193 /usr/include/c++/12/backward 2023-09-12T11:09:37,194 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:37,194 /usr/local/include 2023-09-12T11:09:37,195 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:37,195 /usr/include 2023-09-12T11:09:37,196 End of search list. 2023-09-12T11:09:37,196 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:37,196 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:37,197 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:37,198 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:37,203 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:38,785 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:38,786 from include/openbabel/mol.h:43, 2023-09-12T11:09:38,786 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:38,787 from ./src/formats/painterformat.cpp:19: 2023-09-12T11:09:38,787 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:38,788 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:38,789 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:38,789 | ^ 2023-09-12T11:09:38,790 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:38,790 37 | # define UNUSED(x) x 2023-09-12T11:09:38,791 | ^ 2023-09-12T11:09:39,554 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:39,554 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:39,555 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:39,556 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:39,556 | ^ 2023-09-12T11:09:39,557 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:39,558 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:39,559 | ^~~~~~~~ 2023-09-12T11:09:39,560 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:39,560 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:39,561 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:39,562 | ^ 2023-09-12T11:09:39,562 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:39,563 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:39,564 | ^~~~~~~~ 2023-09-12T11:09:39,579 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:39,580 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:39,581 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:39,582 | ^ 2023-09-12T11:09:39,582 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:39,583 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:39,583 | ^~~~~~~~ 2023-09-12T11:09:39,586 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:39,587 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:39,587 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:39,588 | ^ 2023-09-12T11:09:39,588 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:39,589 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:39,590 | ^~~~~~~~ 2023-09-12T11:09:39,765 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:39,766 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:39,767 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:39,767 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:39,768 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:39,769 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:39,770 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:39,770 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:39,771 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:39,772 from include/openbabel/mol.h:35: 2023-09-12T11:09:39,772 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:39,773 131 | struct binary_function 2023-09-12T11:09:39,774 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:39,994 In file included from ./src/formats/painterformat.cpp:22: 2023-09-12T11:09:39,994 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2023-09-12T11:09:39,995 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T11:09:39,996 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2023-09-12T11:09:39,996 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:09:40,001 ./src/formats/painterformat.cpp: In member function ‘virtual bool OpenBabel::PainterFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:40,002 ./src/formats/painterformat.cpp:113:12: warning: unused variable ‘ofs’ [-Wunused-variable] 2023-09-12T11:09:40,002 113 | ostream& ofs = *pConv->GetOutStream(); 2023-09-12T11:09:40,003 | ^~~ 2023-09-12T11:09:42,402 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/painterformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:42,403 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/painterformat.o /tmp/cch9mnC6.s 2023-09-12T11:09:42,410 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:42,580 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:09:42,580 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:09:42,581 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/painterformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/painterformat.' 2023-09-12T11:09:42,582 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/pcmodelformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/pcmodelformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:09:42,586 Using built-in specs. 2023-09-12T11:09:42,587 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:42,588 Target: arm-linux-gnueabihf 2023-09-12T11:09:42,588 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:09:42,589 Thread model: posix 2023-09-12T11:09:42,590 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:42,590 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:42,591 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pcmodelformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:42,591 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pcmodelformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase pcmodelformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccr2uNFD.s 2023-09-12T11:09:42,600 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:42,601 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:42,602 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:42,603 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:42,603 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:42,603 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:42,604 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:42,604 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:42,605 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:42,605 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:42,606 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:42,607 #include "..." search starts here: 2023-09-12T11:09:42,607 #include <...> search starts here: 2023-09-12T11:09:42,608 /usr/include/eigen3 2023-09-12T11:09:42,608 include 2023-09-12T11:09:42,609 /usr/include/python3.11 2023-09-12T11:09:42,609 /usr/include/c++/12 2023-09-12T11:09:42,610 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:42,611 /usr/include/c++/12/backward 2023-09-12T11:09:42,611 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:42,612 /usr/local/include 2023-09-12T11:09:42,613 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:42,613 /usr/include 2023-09-12T11:09:42,614 End of search list. 2023-09-12T11:09:42,615 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:42,615 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:42,617 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:42,617 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:42,622 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:44,186 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:44,187 from include/openbabel/mol.h:43, 2023-09-12T11:09:44,187 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:44,188 from ./src/formats/pcmodelformat.cpp:16: 2023-09-12T11:09:44,189 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:44,189 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:44,190 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:44,191 | ^ 2023-09-12T11:09:44,191 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:44,192 37 | # define UNUSED(x) x 2023-09-12T11:09:44,193 | ^ 2023-09-12T11:09:44,961 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:44,961 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:44,962 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:44,962 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:44,963 | ^ 2023-09-12T11:09:44,964 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:44,964 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:44,965 | ^~~~~~~~ 2023-09-12T11:09:44,966 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:44,967 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:44,967 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:44,968 | ^ 2023-09-12T11:09:44,968 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:44,969 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:44,970 | ^~~~~~~~ 2023-09-12T11:09:44,985 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:44,986 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:44,987 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:44,988 | ^ 2023-09-12T11:09:44,989 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:44,989 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:44,990 | ^~~~~~~~ 2023-09-12T11:09:44,992 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:44,993 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:44,993 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:44,994 | ^ 2023-09-12T11:09:44,995 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:44,995 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:44,996 | ^~~~~~~~ 2023-09-12T11:09:45,165 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:45,166 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:45,167 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:45,167 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:45,168 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:45,168 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:45,169 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:45,169 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:45,170 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:45,170 from include/openbabel/mol.h:35: 2023-09-12T11:09:45,171 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:45,171 131 | struct binary_function 2023-09-12T11:09:45,172 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:48,389 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pcmodelformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:48,390 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/pcmodelformat.o /tmp/ccr2uNFD.s 2023-09-12T11:09:48,394 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:48,607 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:09:48,608 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:09:48,609 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pcmodelformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/pcmodelformat.' 2023-09-12T11:09:48,609 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/pdbformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/pdbformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:09:48,614 Using built-in specs. 2023-09-12T11:09:48,615 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:48,616 Target: arm-linux-gnueabihf 2023-09-12T11:09:48,616 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:09:48,617 Thread model: posix 2023-09-12T11:09:48,617 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:48,618 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:48,618 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:09:48,619 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pdbformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase pdbformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccGzdWzq.s 2023-09-12T11:09:48,628 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:48,629 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:48,630 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:48,630 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:48,631 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:48,632 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:48,632 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:48,633 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:48,634 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:48,635 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:48,635 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:48,636 #include "..." search starts here: 2023-09-12T11:09:48,637 #include <...> search starts here: 2023-09-12T11:09:48,638 /usr/include/eigen3 2023-09-12T11:09:48,639 include 2023-09-12T11:09:48,640 /usr/include/python3.11 2023-09-12T11:09:48,641 /usr/include/c++/12 2023-09-12T11:09:48,642 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:48,643 /usr/include/c++/12/backward 2023-09-12T11:09:48,644 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:48,644 /usr/local/include 2023-09-12T11:09:48,645 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:48,645 /usr/include 2023-09-12T11:09:48,646 End of search list. 2023-09-12T11:09:48,647 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:48,647 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:48,649 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:48,650 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:48,650 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:50,232 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:50,232 from include/openbabel/mol.h:43, 2023-09-12T11:09:50,233 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:50,233 from ./src/formats/pdbformat.cpp:17: 2023-09-12T11:09:50,234 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:50,235 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:50,235 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:50,236 | ^ 2023-09-12T11:09:50,236 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:50,237 37 | # define UNUSED(x) x 2023-09-12T11:09:50,237 | ^ 2023-09-12T11:09:51,010 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:51,011 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:51,011 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:51,012 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:51,013 | ^ 2023-09-12T11:09:51,013 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:51,014 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:51,015 | ^~~~~~~~ 2023-09-12T11:09:51,016 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:51,017 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:51,018 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:51,018 | ^ 2023-09-12T11:09:51,019 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:51,020 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:51,021 | ^~~~~~~~ 2023-09-12T11:09:51,036 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:51,036 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:51,037 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:51,038 | ^ 2023-09-12T11:09:51,039 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:51,039 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:51,040 | ^~~~~~~~ 2023-09-12T11:09:51,043 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:51,043 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:51,044 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:51,044 | ^ 2023-09-12T11:09:51,045 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:51,045 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:51,046 | ^~~~~~~~ 2023-09-12T11:09:51,218 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:51,219 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:51,219 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:51,220 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:51,220 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:51,221 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:51,221 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:51,222 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:51,223 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:51,223 from include/openbabel/mol.h:35: 2023-09-12T11:09:51,224 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:51,225 131 | struct binary_function 2023-09-12T11:09:51,226 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:54,917 ./src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:54,918 ./src/formats/pdbformat.cpp:623:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:09:54,919 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:09:54,919 | ^ 2023-09-12T11:09:54,920 ./src/formats/pdbformat.cpp:623:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:09:54,921 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:09:54,921 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:54,922 ./src/formats/pdbformat.cpp:641:70: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:09:54,922 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:09:54,923 | ^ 2023-09-12T11:09:54,924 ./src/formats/pdbformat.cpp:641:29: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:09:54,925 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:09:54,925 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:54,926 ./src/formats/pdbformat.cpp:678:35: warning: ‘%+d’ directive output may be truncated writing between 2 and 6 bytes into a region of size 3 [-Wformat-truncation=] 2023-09-12T11:09:54,927 678 | snprintf(scharge, 3, "%+d", charge); 2023-09-12T11:09:54,928 | ^~~ 2023-09-12T11:09:54,929 ./src/formats/pdbformat.cpp:678:34: note: directive argument in the range [-32768, 32767] 2023-09-12T11:09:54,929 678 | snprintf(scharge, 3, "%+d", charge); 2023-09-12T11:09:54,930 | ^~~~~ 2023-09-12T11:09:54,930 ./src/formats/pdbformat.cpp:678:21: note: ‘snprintf’ output between 3 and 7 bytes into a destination of size 3 2023-09-12T11:09:54,931 678 | snprintf(scharge, 3, "%+d", charge); 2023-09-12T11:09:54,931 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:58,396 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:09:58,396 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:347:34, 2023-09-12T11:09:58,397 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:09:58,398 ./src/formats/pdbformat.cpp:261:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 5 bytes from a string of length 32761 [-Wstringop-truncation] 2023-09-12T11:09:58,398 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:09:58,399 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:58,400 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:09:58,401 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:404:66, 2023-09-12T11:09:58,401 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:09:58,402 ./src/formats/pdbformat.cpp:261:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 5 bytes from a string of length 32756 [-Wstringop-truncation] 2023-09-12T11:09:58,403 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:09:58,404 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:58,404 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:09:58,405 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:407:66, 2023-09-12T11:09:58,406 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:09:58,407 ./src/formats/pdbformat.cpp:261:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 5 bytes from a string of length 32751 [-Wstringop-truncation] 2023-09-12T11:09:58,408 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:09:58,409 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:58,411 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:09:58,412 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:408:66, 2023-09-12T11:09:58,413 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:09:58,414 ./src/formats/pdbformat.cpp:261:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 5 bytes from a string of length 32746 [-Wstringop-truncation] 2023-09-12T11:09:58,415 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:09:58,416 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:58,418 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:09:58,419 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:409:66, 2023-09-12T11:09:58,421 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:09:58,421 ./src/formats/pdbformat.cpp:261:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 5 bytes from a string of length 32741 [-Wstringop-truncation] 2023-09-12T11:09:58,422 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:09:58,423 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:00,486 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:00,486 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/pdbformat.o /tmp/ccGzdWzq.s 2023-09-12T11:10:00,491 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:01,168 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:10:01,169 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:10:01,169 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbformat.' 2023-09-12T11:10:01,172 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/pdbqtformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/pdbqtformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:01,176 Using built-in specs. 2023-09-12T11:10:01,176 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:01,177 Target: arm-linux-gnueabihf 2023-09-12T11:10:01,177 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:10:01,178 Thread model: posix 2023-09-12T11:10:01,179 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:01,179 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:01,180 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbqtformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:01,180 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pdbqtformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase pdbqtformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccSPKorA.s 2023-09-12T11:10:01,189 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:01,189 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:01,191 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:01,191 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:01,192 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:01,192 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:01,193 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:01,194 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:01,194 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:01,195 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:01,195 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:01,196 #include "..." search starts here: 2023-09-12T11:10:01,196 #include <...> search starts here: 2023-09-12T11:10:01,197 /usr/include/eigen3 2023-09-12T11:10:01,197 include 2023-09-12T11:10:01,198 /usr/include/python3.11 2023-09-12T11:10:01,198 /usr/include/c++/12 2023-09-12T11:10:01,199 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:01,199 /usr/include/c++/12/backward 2023-09-12T11:10:01,200 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:01,201 /usr/local/include 2023-09-12T11:10:01,201 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:01,202 /usr/include 2023-09-12T11:10:01,202 End of search list. 2023-09-12T11:10:01,203 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:01,203 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:01,205 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:01,205 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:01,207 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:02,779 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:02,780 from include/openbabel/mol.h:43, 2023-09-12T11:10:02,781 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:02,781 from ./src/formats/pdbqtformat.cpp:24: 2023-09-12T11:10:02,782 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:02,782 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:02,783 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:02,784 | ^ 2023-09-12T11:10:02,784 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:02,785 37 | # define UNUSED(x) x 2023-09-12T11:10:02,785 | ^ 2023-09-12T11:10:03,547 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:03,548 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:03,549 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:03,549 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:03,550 | ^ 2023-09-12T11:10:03,551 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:03,551 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:03,552 | ^~~~~~~~ 2023-09-12T11:10:03,553 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:03,553 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:03,554 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:03,555 | ^ 2023-09-12T11:10:03,555 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:03,556 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:03,557 | ^~~~~~~~ 2023-09-12T11:10:03,572 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:03,572 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:03,573 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:03,574 | ^ 2023-09-12T11:10:03,574 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:03,575 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:03,576 | ^~~~~~~~ 2023-09-12T11:10:03,578 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:03,579 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:03,580 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:03,580 | ^ 2023-09-12T11:10:03,581 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:03,582 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:03,582 | ^~~~~~~~ 2023-09-12T11:10:03,752 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:03,752 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:03,753 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:03,754 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:03,754 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:03,755 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:03,755 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:03,756 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:03,756 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:03,757 from include/openbabel/mol.h:35: 2023-09-12T11:10:03,758 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:03,758 131 | struct binary_function 2023-09-12T11:10:03,759 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:04,144 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::OutputTree(OBConversion*, OBMol&, std::ostream&, std::map&, unsigned int, bool, bool)’: 2023-09-12T11:10:04,145 ./src/formats/pdbqtformat.cpp:580:20: warning: unused variable ‘child’ [-Wunused-variable] 2023-09-12T11:10:04,145 580 | unsigned int child=i; 2023-09-12T11:10:04,146 | ^~~~~ 2023-09-12T11:10:04,198 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::ConstructTree(std::map&, std::vector >, unsigned int, const OBMol&, bool)’: 2023-09-12T11:10:04,198 ./src/formats/pdbqtformat.cpp:609:145: warning: unused parameter ‘flexible’ [-Wunused-parameter] 2023-09-12T11:10:04,199 609 | void ConstructTree (map & tree, vector > rigid_fragments, unsigned int root_piece, const OBMol& mol, bool flexible) 2023-09-12T11:10:04,200 | ~~~~~^~~~~~~~ 2023-09-12T11:10:04,217 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::Separate_preserve_charges(OBMol&, std::vector&)’: 2023-09-12T11:10:04,217 ./src/formats/pdbqtformat.cpp:794:9: warning: unused variable ‘fragments’ [-Wunused-variable] 2023-09-12T11:10:04,218 794 | int fragments = 0; 2023-09-12T11:10:04,219 | ^~~~~~~~~ 2023-09-12T11:10:04,286 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::parseAtomRecord(char*, OBMol&, int)’: 2023-09-12T11:10:04,287 ./src/formats/pdbqtformat.cpp:1045:60: warning: unused parameter ‘chainNum’ [-Wunused-parameter] 2023-09-12T11:10:04,288 1045 | static bool parseAtomRecord(char *buffer, OBMol &mol,int chainNum) 2023-09-12T11:10:04,288 | ~~~~^~~~~~~~ 2023-09-12T11:10:05,931 ./src/formats/pdbqtformat.cpp: At global scope: 2023-09-12T11:10:05,932 ./src/formats/pdbqtformat.cpp:747:16: warning: ‘unsigned int OpenBabel::AtomsSoFar(const std::map&, unsigned int)’ defined but not used [-Wunused-function] 2023-09-12T11:10:05,933 747 | unsigned int AtomsSoFar(const map & tree, unsigned int depth) 2023-09-12T11:10:05,933 | ^~~~~~~~~~ 2023-09-12T11:10:08,339 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::OutputAtom(OBAtom*, std::ostream&, unsigned int)’: 2023-09-12T11:10:08,340 ./src/formats/pdbqtformat.cpp:334:52: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:10:08,340 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:10:08,341 | ^ 2023-09-12T11:10:08,342 ./src/formats/pdbqtformat.cpp:334:15: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:10:08,342 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:10:08,343 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:08,343 ./src/formats/pdbqtformat.cpp:351:60: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:10:08,344 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:10:08,345 | ^ 2023-09-12T11:10:08,345 ./src/formats/pdbqtformat.cpp:351:19: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:10:08,346 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:10:08,347 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:10,932 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:10:10,932 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::OBMol&}; _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’: 2023-09-12T11:10:10,933 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:10,934 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:10:10,934 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:15,898 ./src/formats/pdbqtformat.cpp: In member function ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:15,899 ./src/formats/pdbqtformat.cpp:915:22: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 10 equals destination size [-Wstringop-truncation] 2023-09-12T11:10:15,900 915 | strncpy(type_name, etab.GetSymbol(rotBondTable[rotBondId][bondAtomNum]->GetAtomicNum()), sizeof(type_name)); 2023-09-12T11:10:15,901 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:16,034 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:10:16,035 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:10:16,036 inlined from ‘bool OpenBabel::Separate_preserve_charges(OBMol&, std::vector&)’ at ./src/formats/pdbqtformat.cpp:797:23, 2023-09-12T11:10:16,037 inlined from ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbqtformat.cpp:849:32: 2023-09-12T11:10:16,037 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:16,038 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:10:16,039 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:10:16,040 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:10:16,040 inlined from ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbqtformat.cpp:845:27: 2023-09-12T11:10:16,041 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:16,041 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:10:16,042 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:10:18,139 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbqtformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:18,140 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/pdbqtformat.o /tmp/ccSPKorA.s 2023-09-12T11:10:18,145 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:19,154 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:10:19,155 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:10:19,155 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbqtformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/pdbqtformat.' 2023-09-12T11:10:19,159 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/pointcloudformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/pointcloudformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:19,163 Using built-in specs. 2023-09-12T11:10:19,164 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:19,165 Target: arm-linux-gnueabihf 2023-09-12T11:10:19,165 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:10:19,166 Thread model: posix 2023-09-12T11:10:19,167 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:19,167 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:19,167 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pointcloudformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:19,168 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pointcloudformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase pointcloudformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccEnk5sx.s 2023-09-12T11:10:19,176 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:19,177 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:19,178 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:19,179 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:19,179 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:19,180 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:19,180 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:19,181 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:19,182 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:19,182 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:19,183 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:19,183 #include "..." search starts here: 2023-09-12T11:10:19,184 #include <...> search starts here: 2023-09-12T11:10:19,184 /usr/include/eigen3 2023-09-12T11:10:19,185 include 2023-09-12T11:10:19,186 /usr/include/python3.11 2023-09-12T11:10:19,186 /usr/include/c++/12 2023-09-12T11:10:19,187 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:19,187 /usr/include/c++/12/backward 2023-09-12T11:10:19,188 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:19,189 /usr/local/include 2023-09-12T11:10:19,189 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:19,190 /usr/include 2023-09-12T11:10:19,191 End of search list. 2023-09-12T11:10:19,191 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:19,192 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:19,193 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:19,194 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:19,197 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:20,794 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:20,795 from include/openbabel/mol.h:43, 2023-09-12T11:10:20,796 from ./src/formats/pointcloudformat.cpp:28: 2023-09-12T11:10:20,796 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:20,797 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:20,797 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:20,798 | ^ 2023-09-12T11:10:20,798 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:20,799 37 | # define UNUSED(x) x 2023-09-12T11:10:20,799 | ^ 2023-09-12T11:10:21,566 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:21,566 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:21,567 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:21,568 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:21,568 | ^ 2023-09-12T11:10:21,569 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:21,570 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:21,570 | ^~~~~~~~ 2023-09-12T11:10:21,571 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:21,572 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:21,573 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:21,573 | ^ 2023-09-12T11:10:21,574 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:21,575 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:21,576 | ^~~~~~~~ 2023-09-12T11:10:21,591 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:21,592 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:21,593 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:21,593 | ^ 2023-09-12T11:10:21,594 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:21,595 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:21,596 | ^~~~~~~~ 2023-09-12T11:10:21,598 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:21,599 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:21,599 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:21,600 | ^ 2023-09-12T11:10:21,601 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:21,601 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:21,602 | ^~~~~~~~ 2023-09-12T11:10:21,779 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:21,780 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:21,780 from ./src/formats/pointcloudformat.cpp:29: 2023-09-12T11:10:21,781 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:21,781 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:21,782 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:21,783 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:21,783 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:21,784 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:21,784 from include/openbabel/mol.h:35: 2023-09-12T11:10:21,785 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:21,786 131 | struct binary_function 2023-09-12T11:10:21,786 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:21,982 ./src/formats/pointcloudformat.cpp: In member function ‘virtual int OpenBabel::PointCloudFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:10:21,983 ./src/formats/pointcloudformat.cpp:104:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:10:21,983 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:10:21,984 | ~~~~^ 2023-09-12T11:10:21,985 ./src/formats/pointcloudformat.cpp:104:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:10:21,986 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:10:21,986 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:10:22,005 ./src/formats/pointcloudformat.cpp: In member function ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:22,005 ./src/formats/pointcloudformat.cpp:217:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:10:22,006 217 | for( int j = 0; j < radius_mult_list.size(); j++ ) { 2023-09-12T11:10:22,007 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,282 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:10:24,283 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::vector3&}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:10:24,284 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:24,285 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:10:24,285 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,339 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:10:24,339 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:10:24,340 inlined from ‘bool OpenBabel::conditional_add(std::vector&, vector3, double)’ at ./src/formats/pointcloudformat.cpp:150:19: 2023-09-12T11:10:24,340 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:24,341 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:10:24,341 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:10:24,375 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:10:24,376 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:24,376 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:10:24,377 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,427 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:10:24,428 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:24,573 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,574 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:196:63: 2023-09-12T11:10:24,574 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:24,575 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:10:24,575 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:10:24,576 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,577 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:206:59: 2023-09-12T11:10:24,578 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:24,578 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:10:24,579 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:10:24,579 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,580 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:10:24,581 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:211:68: 2023-09-12T11:10:24,582 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:24,583 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,583 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,584 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,584 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:10:24,585 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:213:29: 2023-09-12T11:10:24,585 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:24,586 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,586 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,587 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:10:24,587 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:260:38: 2023-09-12T11:10:24,588 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:24,588 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:10:24,589 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:10:24,933 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pointcloudformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:24,934 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/pointcloudformat.o /tmp/ccEnk5sx.s 2023-09-12T11:10:24,938 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:25,130 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:10:25,130 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:10:25,131 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pointcloudformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/pointcloudformat.' 2023-09-12T11:10:25,131 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/posformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/posformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:25,136 Using built-in specs. 2023-09-12T11:10:25,136 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:25,137 Target: arm-linux-gnueabihf 2023-09-12T11:10:25,137 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:10:25,138 Thread model: posix 2023-09-12T11:10:25,138 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:25,139 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:25,139 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/posformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:25,140 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/posformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase posformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc1uDOpf.s 2023-09-12T11:10:25,149 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:25,149 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:25,150 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:25,151 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:25,151 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:25,152 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:25,152 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:25,153 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:25,154 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:25,155 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:25,155 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:25,156 #include "..." search starts here: 2023-09-12T11:10:25,156 #include <...> search starts here: 2023-09-12T11:10:25,156 /usr/include/eigen3 2023-09-12T11:10:25,157 include 2023-09-12T11:10:25,157 /usr/include/python3.11 2023-09-12T11:10:25,158 /usr/include/c++/12 2023-09-12T11:10:25,158 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:25,158 /usr/include/c++/12/backward 2023-09-12T11:10:25,159 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:25,159 /usr/local/include 2023-09-12T11:10:25,160 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:25,160 /usr/include 2023-09-12T11:10:25,161 End of search list. 2023-09-12T11:10:25,161 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:25,162 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:25,162 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:25,163 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:25,168 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:26,782 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:26,782 from include/openbabel/mol.h:43, 2023-09-12T11:10:26,783 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:26,784 from ./src/formats/posformat.cpp:15: 2023-09-12T11:10:26,784 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:26,785 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:26,785 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:26,786 | ^ 2023-09-12T11:10:26,786 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:26,787 37 | # define UNUSED(x) x 2023-09-12T11:10:26,788 | ^ 2023-09-12T11:10:27,554 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:27,555 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:27,556 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:27,557 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:27,557 | ^ 2023-09-12T11:10:27,558 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:27,559 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:27,559 | ^~~~~~~~ 2023-09-12T11:10:27,560 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:27,561 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:27,561 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:27,562 | ^ 2023-09-12T11:10:27,563 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:27,564 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:27,565 | ^~~~~~~~ 2023-09-12T11:10:27,580 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:27,580 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:27,581 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:27,581 | ^ 2023-09-12T11:10:27,582 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:27,583 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:27,583 | ^~~~~~~~ 2023-09-12T11:10:27,587 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:27,587 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:27,588 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:27,588 | ^ 2023-09-12T11:10:27,589 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:27,590 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:27,590 | ^~~~~~~~ 2023-09-12T11:10:27,766 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:27,773 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:27,774 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:27,775 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:27,775 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:27,776 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:27,777 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:27,777 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:27,778 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:27,779 from include/openbabel/mol.h:35: 2023-09-12T11:10:27,779 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:27,780 131 | struct binary_function 2023-09-12T11:10:27,781 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:27,968 ./src/formats/posformat.cpp: In member function ‘virtual bool OpenBabel::POSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:27,968 ./src/formats/posformat.cpp:101:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:10:27,969 101 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2023-09-12T11:10:27,970 | ~^ ~~~~~~~ 2023-09-12T11:10:27,971 | | | 2023-09-12T11:10:27,971 | | unsigned int* 2023-09-12T11:10:27,972 | int* 2023-09-12T11:10:27,973 | %d 2023-09-12T11:10:31,168 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/posformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:31,168 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/posformat.o /tmp/cc1uDOpf.s 2023-09-12T11:10:31,173 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:31,406 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:10:31,407 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:10:31,407 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/posformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/posformat.' 2023-09-12T11:10:31,408 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/povrayformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/povrayformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:31,412 Using built-in specs. 2023-09-12T11:10:31,413 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:31,414 Target: arm-linux-gnueabihf 2023-09-12T11:10:31,414 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:10:31,415 Thread model: posix 2023-09-12T11:10:31,416 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:31,416 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:31,417 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/povrayformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:31,417 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/povrayformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase povrayformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccVzeIQD.s 2023-09-12T11:10:31,426 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:31,426 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:31,427 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:31,428 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:31,428 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:31,429 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:31,429 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:31,430 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:31,431 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:31,431 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:31,432 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:31,432 #include "..." search starts here: 2023-09-12T11:10:31,433 #include <...> search starts here: 2023-09-12T11:10:31,434 /usr/include/eigen3 2023-09-12T11:10:31,434 include 2023-09-12T11:10:31,435 /usr/include/python3.11 2023-09-12T11:10:31,436 /usr/include/c++/12 2023-09-12T11:10:31,436 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:31,437 /usr/include/c++/12/backward 2023-09-12T11:10:31,437 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:31,438 /usr/local/include 2023-09-12T11:10:31,439 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:31,439 /usr/include 2023-09-12T11:10:31,440 End of search list. 2023-09-12T11:10:31,440 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:31,441 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:31,442 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:31,443 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:31,444 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:33,020 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:33,021 from include/openbabel/mol.h:43, 2023-09-12T11:10:33,022 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:33,022 from ./src/formats/povrayformat.cpp:23: 2023-09-12T11:10:33,023 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:33,024 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:33,024 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:33,025 | ^ 2023-09-12T11:10:33,026 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:33,026 37 | # define UNUSED(x) x 2023-09-12T11:10:33,027 | ^ 2023-09-12T11:10:33,789 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:33,790 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:33,790 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:33,791 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:33,792 | ^ 2023-09-12T11:10:33,792 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:33,793 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:33,793 | ^~~~~~~~ 2023-09-12T11:10:33,794 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:33,795 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:33,796 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:33,796 | ^ 2023-09-12T11:10:33,797 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:33,798 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:33,799 | ^~~~~~~~ 2023-09-12T11:10:33,813 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:33,814 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:33,815 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:33,816 | ^ 2023-09-12T11:10:33,816 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:33,817 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:33,818 | ^~~~~~~~ 2023-09-12T11:10:33,820 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:33,820 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:33,821 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:33,822 | ^ 2023-09-12T11:10:33,823 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:33,823 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:33,824 | ^~~~~~~~ 2023-09-12T11:10:33,994 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:33,994 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:33,995 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:33,995 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:33,996 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:33,996 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:33,997 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:33,997 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:33,998 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:33,998 from include/openbabel/mol.h:35: 2023-09-12T11:10:33,999 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:33,999 131 | struct binary_function 2023-09-12T11:10:34,000 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:34,272 ./src/formats/povrayformat.cpp: In member function ‘void OpenBabel::PovrayFormat::OutputHeader(std::ostream&, OpenBabel::OBMol&, std::string)’: 2023-09-12T11:10:34,273 ./src/formats/povrayformat.cpp:168:12: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:10:34,273 168 | size_t time_res; /* Result of strftime */ 2023-09-12T11:10:34,274 | ^~~~~~~~ 2023-09-12T11:10:34,274 ./src/formats/povrayformat.cpp:164:68: warning: unused parameter ‘prefix’ [-Wunused-parameter] 2023-09-12T11:10:34,275 164 | void PovrayFormat::OutputHeader(ostream &ofs, OBMol &mol, string prefix) 2023-09-12T11:10:34,276 | ~~~~~~~^~~~~~ 2023-09-12T11:10:34,306 ./src/formats/povrayformat.cpp: In function ‘void OpenBabel::OutputCSTBonds(std::ostream&, OBMol&, std::string)’: 2023-09-12T11:10:34,306 ./src/formats/povrayformat.cpp:521:78: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = char]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:10:34,307 521 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2023-09-12T11:10:34,308 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:34,309 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T11:10:34,310 /usr/include/c++/12/backward/binders.h:136:5: note: declared here 2023-09-12T11:10:34,310 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:10:34,311 | ^~~~~~~ 2023-09-12T11:10:34,321 ./src/formats/povrayformat.cpp:582:78: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = char]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:10:34,322 582 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2023-09-12T11:10:34,322 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:34,323 /usr/include/c++/12/backward/binders.h:136:5: note: declared here 2023-09-12T11:10:34,324 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:10:34,325 | ^~~~~~~ 2023-09-12T11:10:34,389 ./src/formats/povrayformat.cpp: In member function ‘virtual bool OpenBabel::PovrayFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:34,389 ./src/formats/povrayformat.cpp:802:17: warning: unused variable ‘title’ [-Wunused-variable] 2023-09-12T11:10:34,390 802 | const char* title = pmol->GetTitle(); 2023-09-12T11:10:34,391 | ^~~~~ 2023-09-12T11:10:40,379 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/povrayformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:40,380 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/povrayformat.o /tmp/ccVzeIQD.s 2023-09-12T11:10:40,384 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:40,835 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:10:40,836 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:10:40,836 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/povrayformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/povrayformat.' 2023-09-12T11:10:40,838 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/pqrformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/pqrformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:40,842 Using built-in specs. 2023-09-12T11:10:40,843 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:40,844 Target: arm-linux-gnueabihf 2023-09-12T11:10:40,844 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:10:40,845 Thread model: posix 2023-09-12T11:10:40,845 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:40,846 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:40,847 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pqrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:40,847 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pqrformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase pqrformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccD9IzJa.s 2023-09-12T11:10:40,855 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:40,856 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:40,857 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:40,857 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:40,858 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:40,859 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:40,859 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:40,860 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:40,860 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:40,861 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:40,861 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:40,862 #include "..." search starts here: 2023-09-12T11:10:40,863 #include <...> search starts here: 2023-09-12T11:10:40,863 /usr/include/eigen3 2023-09-12T11:10:40,864 include 2023-09-12T11:10:40,865 /usr/include/python3.11 2023-09-12T11:10:40,865 /usr/include/c++/12 2023-09-12T11:10:40,866 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:40,867 /usr/include/c++/12/backward 2023-09-12T11:10:40,867 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:40,868 /usr/local/include 2023-09-12T11:10:40,868 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:40,869 /usr/include 2023-09-12T11:10:40,869 End of search list. 2023-09-12T11:10:40,870 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:40,871 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:40,872 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:40,872 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:40,873 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:42,440 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:42,441 from include/openbabel/mol.h:43, 2023-09-12T11:10:42,442 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:42,443 from ./src/formats/pqrformat.cpp:16: 2023-09-12T11:10:42,443 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:42,444 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:42,445 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:42,445 | ^ 2023-09-12T11:10:42,446 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:42,446 37 | # define UNUSED(x) x 2023-09-12T11:10:42,447 | ^ 2023-09-12T11:10:43,208 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:43,209 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:43,209 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:43,210 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:43,211 | ^ 2023-09-12T11:10:43,211 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:43,212 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:43,212 | ^~~~~~~~ 2023-09-12T11:10:43,214 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:43,214 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:43,215 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:43,216 | ^ 2023-09-12T11:10:43,216 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:43,217 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:43,218 | ^~~~~~~~ 2023-09-12T11:10:43,232 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:43,233 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:43,234 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:43,234 | ^ 2023-09-12T11:10:43,235 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:43,236 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:43,236 | ^~~~~~~~ 2023-09-12T11:10:43,239 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:43,240 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:43,240 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:43,241 | ^ 2023-09-12T11:10:43,242 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:43,243 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:43,244 | ^~~~~~~~ 2023-09-12T11:10:43,412 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:43,413 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:43,414 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:43,414 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:43,415 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:43,415 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:43,416 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:43,416 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:43,417 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:43,417 from include/openbabel/mol.h:35: 2023-09-12T11:10:43,418 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:43,419 131 | struct binary_function 2023-09-12T11:10:43,419 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:43,629 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomCharge(char*, OBMol&)’: 2023-09-12T11:10:43,630 ./src/formats/pqrformat.cpp:196:13: warning: unused variable ‘atom’ [-Wunused-variable] 2023-09-12T11:10:43,631 196 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2023-09-12T11:10:43,631 | ^~~~ 2023-09-12T11:10:43,632 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomRadius(char*, OBMol&)’: 2023-09-12T11:10:43,633 ./src/formats/pqrformat.cpp:211:13: warning: unused variable ‘atom’ [-Wunused-variable] 2023-09-12T11:10:43,634 211 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2023-09-12T11:10:43,634 | ^~~~ 2023-09-12T11:10:46,016 ./src/formats/pqrformat.cpp: In member function ‘virtual bool OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:46,017 ./src/formats/pqrformat.cpp:501:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:10:46,017 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:10:46,018 | ^ 2023-09-12T11:10:46,019 ./src/formats/pqrformat.cpp:501:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:10:46,020 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:10:46,020 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:46,021 ./src/formats/pqrformat.cpp:518:66: warning: ‘%-3s’ directive output may be truncated writing between 3 and 15 bytes into a region of size 9 [-Wformat-truncation=] 2023-09-12T11:10:46,021 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:10:46,022 | ^~~~ ~~~ 2023-09-12T11:10:46,023 ./src/formats/pqrformat.cpp:518:29: note: ‘snprintf’ output between 5 and 17 bytes into a destination of size 10 2023-09-12T11:10:46,024 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:10:46,024 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:46,763 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:10:46,764 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:10:46,765 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:46,765 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:10:46,766 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:48,658 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:48,659 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:10:48,660 inlined from ‘virtual bool OpenBabel::PQRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pqrformat.cpp:135:30: 2023-09-12T11:10:48,660 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:48,661 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:48,661 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:48,662 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:48,662 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:10:48,663 inlined from ‘virtual bool OpenBabel::PQRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pqrformat.cpp:136:28: 2023-09-12T11:10:48,664 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:10:48,665 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:48,665 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:49,463 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pqrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:49,464 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/pqrformat.o /tmp/ccD9IzJa.s 2023-09-12T11:10:49,471 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:49,943 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:10:49,943 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:10:49,944 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pqrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/pqrformat.' 2023-09-12T11:10:49,946 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/pwscfformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/pwscfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:49,950 Using built-in specs. 2023-09-12T11:10:49,951 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:49,952 Target: arm-linux-gnueabihf 2023-09-12T11:10:49,952 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:10:49,953 Thread model: posix 2023-09-12T11:10:49,953 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:49,954 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:49,954 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pwscfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:49,955 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pwscfformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase pwscfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccnO44L9.s 2023-09-12T11:10:49,965 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:49,965 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:49,966 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:49,967 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:49,967 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:49,968 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:49,968 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:49,969 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:49,969 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:49,970 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:49,970 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:49,971 #include "..." search starts here: 2023-09-12T11:10:49,971 #include <...> search starts here: 2023-09-12T11:10:49,971 /usr/include/eigen3 2023-09-12T11:10:49,972 include 2023-09-12T11:10:49,972 /usr/include/python3.11 2023-09-12T11:10:49,973 /usr/include/c++/12 2023-09-12T11:10:49,973 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:49,974 /usr/include/c++/12/backward 2023-09-12T11:10:49,974 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:49,974 /usr/local/include 2023-09-12T11:10:49,975 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:49,975 /usr/include 2023-09-12T11:10:49,976 End of search list. 2023-09-12T11:10:49,976 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:49,977 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:49,978 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:49,978 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:49,985 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:51,548 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:51,549 from include/openbabel/mol.h:43, 2023-09-12T11:10:51,549 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:51,550 from ./src/formats/pwscfformat.cpp:16: 2023-09-12T11:10:51,551 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:51,552 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:51,552 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:51,553 | ^ 2023-09-12T11:10:51,554 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:51,555 37 | # define UNUSED(x) x 2023-09-12T11:10:51,555 | ^ 2023-09-12T11:10:52,317 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:52,318 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:52,318 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:52,319 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:52,320 | ^ 2023-09-12T11:10:52,321 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:52,321 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:52,322 | ^~~~~~~~ 2023-09-12T11:10:52,323 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:52,324 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:52,324 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:52,326 | ^ 2023-09-12T11:10:52,326 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:52,327 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:52,327 | ^~~~~~~~ 2023-09-12T11:10:52,342 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:52,342 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:52,343 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:52,343 | ^ 2023-09-12T11:10:52,344 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:52,344 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:52,345 | ^~~~~~~~ 2023-09-12T11:10:52,348 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:52,348 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:52,349 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:52,350 | ^ 2023-09-12T11:10:52,350 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:52,351 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:52,352 | ^~~~~~~~ 2023-09-12T11:10:52,520 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:52,521 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:52,522 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:52,522 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:52,523 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:52,524 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:52,525 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:52,525 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:52,526 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:52,527 from include/openbabel/mol.h:35: 2023-09-12T11:10:52,527 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:52,528 131 | struct binary_function 2023-09-12T11:10:52,529 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:52,719 ./src/formats/pwscfformat.cpp: In member function ‘virtual int OpenBabel::PWscfFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:10:52,720 ./src/formats/pwscfformat.cpp:51:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:10:52,721 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:10:52,722 | ~~~~^ 2023-09-12T11:10:52,723 ./src/formats/pwscfformat.cpp:51:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:10:52,723 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:10:52,724 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:10:55,320 ./src/formats/pwscfformat.cpp: In member function ‘virtual bool OpenBabel::PWscfFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:55,321 ./src/formats/pwscfformat.cpp:276:15: warning: ‘pv’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:10:55,322 276 | snprintf(tag, BUFF_SIZE, "%f", pv_kcal_per_mole); 2023-09-12T11:10:55,322 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:55,323 ./src/formats/pwscfformat.cpp:90:22: note: ‘pv’ was declared here 2023-09-12T11:10:55,324 90 | double enthalpy, pv; 2023-09-12T11:10:55,324 | ^~ 2023-09-12T11:10:55,325 ./src/formats/pwscfformat.cpp:274:15: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:10:55,325 274 | snprintf(tag, BUFF_SIZE, "%f", en_kcal_per_mole); 2023-09-12T11:10:55,326 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:55,327 ./src/formats/pwscfformat.cpp:90:12: note: ‘enthalpy’ was declared here 2023-09-12T11:10:55,327 90 | double enthalpy, pv; 2023-09-12T11:10:55,328 | ^~~~~~~~ 2023-09-12T11:10:56,171 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pwscfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:56,171 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/pwscfformat.o /tmp/ccnO44L9.s 2023-09-12T11:10:56,176 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:56,412 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:10:56,413 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:10:56,414 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/pwscfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/pwscfformat.' 2023-09-12T11:10:56,415 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/qchemformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/qchemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:56,419 Using built-in specs. 2023-09-12T11:10:56,419 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:56,420 Target: arm-linux-gnueabihf 2023-09-12T11:10:56,420 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:10:56,421 Thread model: posix 2023-09-12T11:10:56,421 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:56,422 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:56,422 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/qchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:10:56,423 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/qchemformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase qchemformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc62VnIA.s 2023-09-12T11:10:56,431 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:56,432 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:56,433 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:56,433 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:56,434 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:56,434 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:56,435 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:56,435 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:56,436 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:56,437 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:56,437 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:56,438 #include "..." search starts here: 2023-09-12T11:10:56,438 #include <...> search starts here: 2023-09-12T11:10:56,439 /usr/include/eigen3 2023-09-12T11:10:56,440 include 2023-09-12T11:10:56,440 /usr/include/python3.11 2023-09-12T11:10:56,441 /usr/include/c++/12 2023-09-12T11:10:56,441 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:56,442 /usr/include/c++/12/backward 2023-09-12T11:10:56,442 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:56,443 /usr/local/include 2023-09-12T11:10:56,443 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:56,444 /usr/include 2023-09-12T11:10:56,444 End of search list. 2023-09-12T11:10:56,445 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:56,445 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:56,446 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:56,446 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:56,451 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:58,012 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:58,013 from include/openbabel/mol.h:43, 2023-09-12T11:10:58,013 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:58,014 from ./src/formats/qchemformat.cpp:17: 2023-09-12T11:10:58,014 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:58,015 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:58,015 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:58,016 | ^ 2023-09-12T11:10:58,016 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:58,017 37 | # define UNUSED(x) x 2023-09-12T11:10:58,018 | ^ 2023-09-12T11:10:58,780 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:58,781 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:58,781 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:58,782 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:58,783 | ^ 2023-09-12T11:10:58,783 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:58,784 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:58,785 | ^~~~~~~~ 2023-09-12T11:10:58,786 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:58,786 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:58,787 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:58,788 | ^ 2023-09-12T11:10:58,788 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:58,789 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:58,789 | ^~~~~~~~ 2023-09-12T11:10:58,805 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:58,805 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:58,806 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:58,807 | ^ 2023-09-12T11:10:58,808 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:58,808 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:58,809 | ^~~~~~~~ 2023-09-12T11:10:58,812 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:58,813 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:58,813 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:58,814 | ^ 2023-09-12T11:10:58,814 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:58,815 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:58,815 | ^~~~~~~~ 2023-09-12T11:10:58,986 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:58,987 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:58,987 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:58,988 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:58,989 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:58,989 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:58,990 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:58,991 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:58,992 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:58,993 from include/openbabel/mol.h:35: 2023-09-12T11:10:58,993 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:58,994 131 | struct binary_function 2023-09-12T11:10:58,995 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:02,451 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:11:02,451 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:11:02,452 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:11:02,452 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:11:02,453 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:02,512 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:11:02,512 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:11:03,386 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:11:03,387 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:11:03,388 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:217:36: 2023-09-12T11:11:03,388 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:11:03,389 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:11:03,389 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:03,390 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:11:03,391 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:11:03,391 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:227:36: 2023-09-12T11:11:03,392 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:11:03,392 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:11:03,393 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:03,394 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:11:03,395 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:11:03,395 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:245:33: 2023-09-12T11:11:03,396 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:11:03,397 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:11:03,398 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:03,398 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:11:03,399 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:11:03,400 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:247:33: 2023-09-12T11:11:03,400 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:11:03,401 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:11:03,402 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:03,402 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:11:03,403 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:11:03,404 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:249:33: 2023-09-12T11:11:03,405 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:11:03,406 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:11:03,406 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:04,679 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/qchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:04,680 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/qchemformat.o /tmp/cc62VnIA.s 2023-09-12T11:11:04,684 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:11:05,093 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:11:05,094 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:11:05,094 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/qchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/qchemformat.' 2023-09-12T11:11:05,096 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/reportformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/reportformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:11:05,101 Using built-in specs. 2023-09-12T11:11:05,101 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:11:05,102 Target: arm-linux-gnueabihf 2023-09-12T11:11:05,103 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:11:05,103 Thread model: posix 2023-09-12T11:11:05,104 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:11:05,104 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:11:05,105 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/reportformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:05,105 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/reportformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase reportformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccpINkJ2.s 2023-09-12T11:11:05,114 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:05,115 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:05,116 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:05,116 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:05,117 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:11:05,118 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:11:05,118 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:11:05,119 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:11:05,120 ignoring duplicate directory "/usr/include/" 2023-09-12T11:11:05,120 as it is a non-system directory that duplicates a system directory 2023-09-12T11:11:05,121 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:11:05,121 #include "..." search starts here: 2023-09-12T11:11:05,122 #include <...> search starts here: 2023-09-12T11:11:05,123 /usr/include/eigen3 2023-09-12T11:11:05,123 include 2023-09-12T11:11:05,124 /usr/include/python3.11 2023-09-12T11:11:05,124 /usr/include/c++/12 2023-09-12T11:11:05,125 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:11:05,125 /usr/include/c++/12/backward 2023-09-12T11:11:05,126 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:11:05,127 /usr/local/include 2023-09-12T11:11:05,127 /usr/include/arm-linux-gnueabihf 2023-09-12T11:11:05,128 /usr/include 2023-09-12T11:11:05,129 End of search list. 2023-09-12T11:11:05,129 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:05,130 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:05,131 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:05,132 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:05,134 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:11:06,719 In file included from include/openbabel/atom.h:33, 2023-09-12T11:11:06,720 from include/openbabel/mol.h:43, 2023-09-12T11:11:06,720 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:11:06,721 from ./src/formats/reportformat.cpp:23: 2023-09-12T11:11:06,721 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:11:06,722 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:11:06,722 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:11:06,723 | ^ 2023-09-12T11:11:06,723 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:11:06,724 37 | # define UNUSED(x) x 2023-09-12T11:11:06,725 | ^ 2023-09-12T11:11:07,498 In file included from include/openbabel/mol.h:52: 2023-09-12T11:11:07,499 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:07,499 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:07,500 862 | {return new OBVibrationData(*this);} 2023-09-12T11:11:07,501 | ^ 2023-09-12T11:11:07,501 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:11:07,502 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:11:07,503 | ^~~~~~~~ 2023-09-12T11:11:07,504 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:07,505 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:07,506 907 | {return new OBDOSData(*this);} 2023-09-12T11:11:07,506 | ^ 2023-09-12T11:11:07,507 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:11:07,508 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:11:07,509 | ^~~~~~~~ 2023-09-12T11:11:07,524 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:07,524 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:07,525 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:11:07,526 | ^ 2023-09-12T11:11:07,526 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:11:07,527 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:11:07,528 | ^~~~~~~~ 2023-09-12T11:11:07,531 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:07,531 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:07,532 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:11:07,533 | ^ 2023-09-12T11:11:07,534 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:11:07,534 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:11:07,535 | ^~~~~~~~ 2023-09-12T11:11:07,705 In file included from include/openbabel/format.h:22, 2023-09-12T11:11:07,705 from include/openbabel/obconversion.h:37, 2023-09-12T11:11:07,706 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:11:07,706 include/openbabel/plugin.h: At global scope: 2023-09-12T11:11:07,707 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:11:07,707 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:11:07,708 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:07,709 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:11:07,710 from /usr/include/c++/12/vector:66, 2023-09-12T11:11:07,710 from include/openbabel/mol.h:35: 2023-09-12T11:11:07,711 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:11:07,712 131 | struct binary_function 2023-09-12T11:11:07,712 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:10,727 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/reportformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:10,727 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/reportformat.o /tmp/ccpINkJ2.s 2023-09-12T11:11:10,732 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:11:10,924 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:11:10,925 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:11:10,926 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/reportformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/reportformat.' 2023-09-12T11:11:10,927 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/rsmiformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/rsmiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:11:10,930 Using built-in specs. 2023-09-12T11:11:10,931 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:11:10,932 Target: arm-linux-gnueabihf 2023-09-12T11:11:10,932 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:11:10,932 Thread model: posix 2023-09-12T11:11:10,933 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:11:10,934 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:11:10,934 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/rsmiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:10,934 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/rsmiformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase rsmiformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccxusaAb.s 2023-09-12T11:11:10,945 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:10,946 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:10,947 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:10,947 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:10,948 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:11:10,948 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:11:10,949 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:11:10,950 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:11:10,950 ignoring duplicate directory "/usr/include/" 2023-09-12T11:11:10,951 as it is a non-system directory that duplicates a system directory 2023-09-12T11:11:10,952 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:11:10,952 #include "..." search starts here: 2023-09-12T11:11:10,953 #include <...> search starts here: 2023-09-12T11:11:10,953 /usr/include/eigen3 2023-09-12T11:11:10,953 include 2023-09-12T11:11:10,954 /usr/include/python3.11 2023-09-12T11:11:10,954 /usr/include/c++/12 2023-09-12T11:11:10,955 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:11:10,955 /usr/include/c++/12/backward 2023-09-12T11:11:10,956 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:11:10,956 /usr/local/include 2023-09-12T11:11:10,956 /usr/include/arm-linux-gnueabihf 2023-09-12T11:11:10,957 /usr/include 2023-09-12T11:11:10,957 End of search list. 2023-09-12T11:11:10,958 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:10,958 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:10,959 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:10,959 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:10,965 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:11:12,669 In file included from include/openbabel/atom.h:33, 2023-09-12T11:11:12,669 from include/openbabel/mol.h:43, 2023-09-12T11:11:12,670 from ./src/formats/rsmiformat.cpp:19: 2023-09-12T11:11:12,670 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:11:12,671 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:11:12,672 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:11:12,672 | ^ 2023-09-12T11:11:12,673 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:11:12,674 37 | # define UNUSED(x) x 2023-09-12T11:11:12,675 | ^ 2023-09-12T11:11:13,440 In file included from include/openbabel/mol.h:52: 2023-09-12T11:11:13,441 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:13,441 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:13,442 862 | {return new OBVibrationData(*this);} 2023-09-12T11:11:13,443 | ^ 2023-09-12T11:11:13,444 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:11:13,444 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:11:13,445 | ^~~~~~~~ 2023-09-12T11:11:13,447 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:13,447 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:13,448 907 | {return new OBDOSData(*this);} 2023-09-12T11:11:13,449 | ^ 2023-09-12T11:11:13,450 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:11:13,450 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:11:13,451 | ^~~~~~~~ 2023-09-12T11:11:13,467 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:13,468 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:13,468 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:11:13,469 | ^ 2023-09-12T11:11:13,469 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:11:13,470 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:11:13,470 | ^~~~~~~~ 2023-09-12T11:11:13,474 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:13,475 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:13,476 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:11:13,476 | ^ 2023-09-12T11:11:13,477 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:11:13,477 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:11:13,478 | ^~~~~~~~ 2023-09-12T11:11:13,648 In file included from include/openbabel/format.h:22, 2023-09-12T11:11:13,649 from include/openbabel/obconversion.h:37, 2023-09-12T11:11:13,650 from ./src/formats/rsmiformat.cpp:20: 2023-09-12T11:11:13,651 include/openbabel/plugin.h: At global scope: 2023-09-12T11:11:13,651 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:11:13,652 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:11:13,653 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:13,654 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:11:13,654 from ./src/formats/rsmiformat.cpp:17: 2023-09-12T11:11:13,655 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:11:13,656 131 | struct binary_function 2023-09-12T11:11:13,656 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:19,490 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/rsmiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:19,491 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/rsmiformat.o /tmp/ccxusaAb.s 2023-09-12T11:11:19,495 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:11:19,963 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:11:19,964 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:11:19,964 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/rsmiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/rsmiformat.' 2023-09-12T11:11:19,967 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/rxnformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/rxnformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:11:19,971 Using built-in specs. 2023-09-12T11:11:19,972 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:11:19,972 Target: arm-linux-gnueabihf 2023-09-12T11:11:19,973 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:11:19,973 Thread model: posix 2023-09-12T11:11:19,974 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:11:19,974 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:11:19,975 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/rxnformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:19,975 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/rxnformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase rxnformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccHiHFd6.s 2023-09-12T11:11:19,984 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:19,985 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:19,986 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:19,986 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:19,987 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:11:19,987 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:11:19,987 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:11:19,988 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:11:19,988 ignoring duplicate directory "/usr/include/" 2023-09-12T11:11:19,989 as it is a non-system directory that duplicates a system directory 2023-09-12T11:11:19,989 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:11:19,990 #include "..." search starts here: 2023-09-12T11:11:19,990 #include <...> search starts here: 2023-09-12T11:11:19,991 /usr/include/eigen3 2023-09-12T11:11:19,991 include 2023-09-12T11:11:19,991 /usr/include/python3.11 2023-09-12T11:11:19,992 /usr/include/c++/12 2023-09-12T11:11:19,992 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:11:19,993 /usr/include/c++/12/backward 2023-09-12T11:11:19,993 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:11:19,994 /usr/local/include 2023-09-12T11:11:19,994 /usr/include/arm-linux-gnueabihf 2023-09-12T11:11:19,994 /usr/include 2023-09-12T11:11:19,995 End of search list. 2023-09-12T11:11:19,996 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:19,996 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:19,997 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:19,998 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:20,005 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:11:21,705 In file included from include/openbabel/atom.h:33, 2023-09-12T11:11:21,706 from include/openbabel/mol.h:43, 2023-09-12T11:11:21,707 from ./src/formats/rxnformat.cpp:20: 2023-09-12T11:11:21,708 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:11:21,708 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:11:21,709 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:11:21,710 | ^ 2023-09-12T11:11:21,710 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:11:21,711 37 | # define UNUSED(x) x 2023-09-12T11:11:21,712 | ^ 2023-09-12T11:11:22,479 In file included from include/openbabel/mol.h:52: 2023-09-12T11:11:22,480 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:22,481 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:22,481 862 | {return new OBVibrationData(*this);} 2023-09-12T11:11:22,482 | ^ 2023-09-12T11:11:22,483 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:11:22,484 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:11:22,484 | ^~~~~~~~ 2023-09-12T11:11:22,486 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:22,486 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:22,487 907 | {return new OBDOSData(*this);} 2023-09-12T11:11:22,487 | ^ 2023-09-12T11:11:22,488 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:11:22,489 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:11:22,489 | ^~~~~~~~ 2023-09-12T11:11:22,506 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:22,506 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:22,507 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:11:22,507 | ^ 2023-09-12T11:11:22,508 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:11:22,509 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:11:22,509 | ^~~~~~~~ 2023-09-12T11:11:22,513 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:22,514 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:22,514 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:11:22,515 | ^ 2023-09-12T11:11:22,515 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:11:22,516 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:11:22,517 | ^~~~~~~~ 2023-09-12T11:11:22,687 In file included from include/openbabel/format.h:22, 2023-09-12T11:11:22,688 from include/openbabel/obconversion.h:37, 2023-09-12T11:11:22,689 from ./src/formats/rxnformat.cpp:21: 2023-09-12T11:11:22,689 include/openbabel/plugin.h: At global scope: 2023-09-12T11:11:22,690 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:11:22,691 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:11:22,691 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:22,692 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:11:22,693 from ./src/formats/rxnformat.cpp:17: 2023-09-12T11:11:22,694 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:11:22,694 131 | struct binary_function 2023-09-12T11:11:22,695 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:23,053 ./src/formats/rxnformat.cpp: In member function ‘virtual bool OpenBabel::RXNFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:11:23,054 ./src/formats/rxnformat.cpp:228:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:11:23,055 228 | for(i=0;iNumReactants();i++) 2023-09-12T11:11:23,055 | ~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:23,056 ./src/formats/rxnformat.cpp:235:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:11:23,056 235 | for(i=0;iNumProducts();i++) 2023-09-12T11:11:23,057 | ~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:27,311 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/rxnformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:27,312 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/rxnformat.o /tmp/ccHiHFd6.s 2023-09-12T11:11:27,316 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:11:27,644 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:11:27,645 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:11:27,645 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/rxnformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/rxnformat.' 2023-09-12T11:11:27,647 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/shelxformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/shelxformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:11:27,651 Using built-in specs. 2023-09-12T11:11:27,652 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:11:27,652 Target: arm-linux-gnueabihf 2023-09-12T11:11:27,653 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:11:27,653 Thread model: posix 2023-09-12T11:11:27,654 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:11:27,655 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:11:27,655 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/shelxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:27,656 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/shelxformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase shelxformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cccKt7ok.s 2023-09-12T11:11:27,664 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:27,665 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:27,666 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:27,667 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:27,667 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:11:27,668 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:11:27,669 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:11:27,669 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:11:27,670 ignoring duplicate directory "/usr/include/" 2023-09-12T11:11:27,671 as it is a non-system directory that duplicates a system directory 2023-09-12T11:11:27,671 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:11:27,672 #include "..." search starts here: 2023-09-12T11:11:27,672 #include <...> search starts here: 2023-09-12T11:11:27,673 /usr/include/eigen3 2023-09-12T11:11:27,673 include 2023-09-12T11:11:27,674 /usr/include/python3.11 2023-09-12T11:11:27,674 /usr/include/c++/12 2023-09-12T11:11:27,675 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:11:27,676 /usr/include/c++/12/backward 2023-09-12T11:11:27,676 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:11:27,677 /usr/local/include 2023-09-12T11:11:27,678 /usr/include/arm-linux-gnueabihf 2023-09-12T11:11:27,678 /usr/include 2023-09-12T11:11:27,679 End of search list. 2023-09-12T11:11:27,679 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:27,680 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:27,681 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:27,682 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:27,684 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:11:29,357 In file included from include/openbabel/atom.h:33, 2023-09-12T11:11:29,358 from include/openbabel/mol.h:43, 2023-09-12T11:11:29,358 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:11:29,359 from ./src/formats/shelxformat.cpp:18: 2023-09-12T11:11:29,360 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:11:29,360 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:11:29,361 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:11:29,361 | ^ 2023-09-12T11:11:29,362 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:11:29,362 37 | # define UNUSED(x) x 2023-09-12T11:11:29,363 | ^ 2023-09-12T11:11:30,027 In file included from include/openbabel/mol.h:52: 2023-09-12T11:11:30,027 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:30,028 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:30,029 862 | {return new OBVibrationData(*this);} 2023-09-12T11:11:30,029 | ^ 2023-09-12T11:11:30,030 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:11:30,031 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:11:30,031 | ^~~~~~~~ 2023-09-12T11:11:30,033 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:30,033 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:30,034 907 | {return new OBDOSData(*this);} 2023-09-12T11:11:30,035 | ^ 2023-09-12T11:11:30,036 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:11:30,036 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:11:30,037 | ^~~~~~~~ 2023-09-12T11:11:30,052 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:30,053 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:30,053 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:11:30,054 | ^ 2023-09-12T11:11:30,055 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:11:30,055 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:11:30,056 | ^~~~~~~~ 2023-09-12T11:11:30,059 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:30,060 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:30,060 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:11:30,061 | ^ 2023-09-12T11:11:30,061 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:11:30,062 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:11:30,062 | ^~~~~~~~ 2023-09-12T11:11:30,241 In file included from include/openbabel/format.h:22, 2023-09-12T11:11:30,242 from include/openbabel/obconversion.h:37, 2023-09-12T11:11:30,242 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:11:30,243 include/openbabel/plugin.h: At global scope: 2023-09-12T11:11:30,244 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:11:30,244 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:11:30,245 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:30,246 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:11:30,246 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:11:30,247 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:11:30,248 from /usr/include/c++/12/ios:42, 2023-09-12T11:11:30,249 from /usr/include/c++/12/ostream:38, 2023-09-12T11:11:30,249 from include/openbabel/math/matrix3x3.h:24, 2023-09-12T11:11:30,250 from ./src/formats/shelxformat.cpp:17: 2023-09-12T11:11:30,250 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:11:30,251 131 | struct binary_function 2023-09-12T11:11:30,252 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:32,969 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/shelxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:32,970 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/shelxformat.o /tmp/cccKt7ok.s 2023-09-12T11:11:32,975 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:11:33,142 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:11:33,143 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:11:33,144 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/shelxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/shelxformat.' 2023-09-12T11:11:33,144 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/siestaformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/siestaformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:11:33,148 Using built-in specs. 2023-09-12T11:11:33,149 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:11:33,150 Target: arm-linux-gnueabihf 2023-09-12T11:11:33,150 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:11:33,151 Thread model: posix 2023-09-12T11:11:33,151 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:11:33,152 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:11:33,152 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/siestaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:33,153 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/siestaformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase siestaformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccYw9aOv.s 2023-09-12T11:11:33,161 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:33,162 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:33,163 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:33,164 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:33,164 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:11:33,165 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:11:33,165 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:11:33,166 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:11:33,166 ignoring duplicate directory "/usr/include/" 2023-09-12T11:11:33,167 as it is a non-system directory that duplicates a system directory 2023-09-12T11:11:33,167 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:11:33,168 #include "..." search starts here: 2023-09-12T11:11:33,168 #include <...> search starts here: 2023-09-12T11:11:33,169 /usr/include/eigen3 2023-09-12T11:11:33,169 include 2023-09-12T11:11:33,170 /usr/include/python3.11 2023-09-12T11:11:33,170 /usr/include/c++/12 2023-09-12T11:11:33,170 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:11:33,171 /usr/include/c++/12/backward 2023-09-12T11:11:33,171 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:11:33,172 /usr/local/include 2023-09-12T11:11:33,172 /usr/include/arm-linux-gnueabihf 2023-09-12T11:11:33,173 /usr/include 2023-09-12T11:11:33,173 End of search list. 2023-09-12T11:11:33,174 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:33,174 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:33,176 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:33,176 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:33,179 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:11:34,746 In file included from include/openbabel/atom.h:33, 2023-09-12T11:11:34,746 from include/openbabel/mol.h:43, 2023-09-12T11:11:34,747 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:11:34,748 from ./src/formats/siestaformat.cpp:16: 2023-09-12T11:11:34,749 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:11:34,750 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:11:34,750 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:11:34,751 | ^ 2023-09-12T11:11:34,752 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:11:34,752 37 | # define UNUSED(x) x 2023-09-12T11:11:34,753 | ^ 2023-09-12T11:11:35,514 In file included from include/openbabel/mol.h:52: 2023-09-12T11:11:35,515 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:35,516 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:35,516 862 | {return new OBVibrationData(*this);} 2023-09-12T11:11:35,517 | ^ 2023-09-12T11:11:35,518 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:11:35,519 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:11:35,519 | ^~~~~~~~ 2023-09-12T11:11:35,520 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:35,521 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:35,522 907 | {return new OBDOSData(*this);} 2023-09-12T11:11:35,522 | ^ 2023-09-12T11:11:35,523 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:11:35,524 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:11:35,524 | ^~~~~~~~ 2023-09-12T11:11:35,539 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:35,539 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:35,540 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:11:35,540 | ^ 2023-09-12T11:11:35,541 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:11:35,541 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:11:35,542 | ^~~~~~~~ 2023-09-12T11:11:35,545 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:35,545 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:35,546 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:11:35,547 | ^ 2023-09-12T11:11:35,548 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:11:35,548 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:11:35,549 | ^~~~~~~~ 2023-09-12T11:11:35,718 In file included from include/openbabel/format.h:22, 2023-09-12T11:11:35,719 from include/openbabel/obconversion.h:37, 2023-09-12T11:11:35,719 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:11:35,720 include/openbabel/plugin.h: At global scope: 2023-09-12T11:11:35,720 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:11:35,721 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:11:35,722 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:35,722 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:11:35,723 from /usr/include/c++/12/vector:66, 2023-09-12T11:11:35,724 from include/openbabel/mol.h:35: 2023-09-12T11:11:35,724 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:11:35,725 131 | struct binary_function 2023-09-12T11:11:35,726 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:35,917 ./src/formats/siestaformat.cpp: In member function ‘virtual int OpenBabel::SIESTAFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:11:35,918 ./src/formats/siestaformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:11:35,919 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:11:35,919 | ~~~~^ 2023-09-12T11:11:35,920 ./src/formats/siestaformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:11:35,920 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:11:35,921 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:11:35,982 ./src/formats/siestaformat.cpp: In member function ‘virtual bool OpenBabel::SIESTAFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:11:35,982 ./src/formats/siestaformat.cpp:82:10: warning: variable ‘coordsAreAngstrom’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:11:35,983 82 | bool coordsAreAngstrom = false; 2023-09-12T11:11:35,983 | ^~~~~~~~~~~~~~~~~ 2023-09-12T11:11:35,984 ./src/formats/siestaformat.cpp:88:12: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:11:35,984 88 | size_t size; 2023-09-12T11:11:35,985 | ^~~~ 2023-09-12T11:11:35,985 ./src/formats/siestaformat.cpp:92:30: warning: unused variable ‘numSpecies’ [-Wunused-variable] 2023-09-12T11:11:35,986 92 | int atomicNum, numAtoms, numSpecies; 2023-09-12T11:11:35,986 | ^~~~~~~~~~ 2023-09-12T11:11:41,820 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/siestaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:41,821 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/siestaformat.o /tmp/ccYw9aOv.s 2023-09-12T11:11:41,826 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:11:42,225 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:11:42,225 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:11:42,226 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/siestaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/siestaformat.' 2023-09-12T11:11:42,228 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/smileyformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/smileyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:11:42,232 Using built-in specs. 2023-09-12T11:11:42,233 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:11:42,233 Target: arm-linux-gnueabihf 2023-09-12T11:11:42,234 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:11:42,234 Thread model: posix 2023-09-12T11:11:42,235 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:11:42,235 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:11:42,236 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/smileyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:42,236 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/smileyformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase smileyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccwofxZf.s 2023-09-12T11:11:42,245 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:42,246 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:42,247 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:42,247 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:42,248 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:11:42,248 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:11:42,249 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:11:42,249 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:11:42,250 ignoring duplicate directory "/usr/include/" 2023-09-12T11:11:42,251 as it is a non-system directory that duplicates a system directory 2023-09-12T11:11:42,251 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:11:42,252 #include "..." search starts here: 2023-09-12T11:11:42,252 #include <...> search starts here: 2023-09-12T11:11:42,253 /usr/include/eigen3 2023-09-12T11:11:42,254 include 2023-09-12T11:11:42,254 /usr/include/python3.11 2023-09-12T11:11:42,255 /usr/include/c++/12 2023-09-12T11:11:42,256 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:11:42,256 /usr/include/c++/12/backward 2023-09-12T11:11:42,257 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:11:42,257 /usr/local/include 2023-09-12T11:11:42,257 /usr/include/arm-linux-gnueabihf 2023-09-12T11:11:42,258 /usr/include 2023-09-12T11:11:42,258 End of search list. 2023-09-12T11:11:42,259 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:42,259 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:42,260 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:42,260 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:42,265 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:11:43,857 In file included from include/openbabel/atom.h:33, 2023-09-12T11:11:43,858 from include/openbabel/mol.h:43, 2023-09-12T11:11:43,858 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:11:43,859 from ./src/formats/smileyformat.cpp:15: 2023-09-12T11:11:43,859 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:11:43,860 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:11:43,860 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:11:43,861 | ^ 2023-09-12T11:11:43,862 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:11:43,862 37 | # define UNUSED(x) x 2023-09-12T11:11:43,863 | ^ 2023-09-12T11:11:44,637 In file included from include/openbabel/mol.h:52: 2023-09-12T11:11:44,637 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:44,638 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:44,639 862 | {return new OBVibrationData(*this);} 2023-09-12T11:11:44,639 | ^ 2023-09-12T11:11:44,640 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:11:44,640 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:11:44,641 | ^~~~~~~~ 2023-09-12T11:11:44,643 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:44,644 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:44,644 907 | {return new OBDOSData(*this);} 2023-09-12T11:11:44,645 | ^ 2023-09-12T11:11:44,645 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:11:44,646 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:11:44,647 | ^~~~~~~~ 2023-09-12T11:11:44,663 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:44,663 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:44,664 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:11:44,665 | ^ 2023-09-12T11:11:44,666 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:11:44,666 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:11:44,667 | ^~~~~~~~ 2023-09-12T11:11:44,670 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:44,670 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:44,671 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:11:44,672 | ^ 2023-09-12T11:11:44,672 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:11:44,673 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:11:44,673 | ^~~~~~~~ 2023-09-12T11:11:44,843 In file included from include/openbabel/format.h:22, 2023-09-12T11:11:44,844 from include/openbabel/obconversion.h:37, 2023-09-12T11:11:44,845 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:11:44,845 include/openbabel/plugin.h: At global scope: 2023-09-12T11:11:44,846 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:11:44,847 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:11:44,848 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:44,848 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:11:44,849 from /usr/include/c++/12/vector:66, 2023-09-12T11:11:44,850 from include/openbabel/mol.h:35: 2023-09-12T11:11:44,851 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:11:44,851 131 | struct binary_function 2023-09-12T11:11:44,852 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:45,192 In file included from ./src/formats/smileyformat.cpp:20: 2023-09-12T11:11:45,193 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setChiral(int, Smiley::Chirality, const std::vector&)’: 2023-09-12T11:11:45,193 include/formats/smiley.h:649:24: warning: unused parameter ‘index’ [-Wunused-parameter] 2023-09-12T11:11:45,194 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2023-09-12T11:11:45,195 | ~~~~^~~~~ 2023-09-12T11:11:45,195 include/formats/smiley.h:649:41: warning: unused parameter ‘chirality’ [-Wunused-parameter] 2023-09-12T11:11:45,196 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2023-09-12T11:11:45,197 | ~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:11:45,197 include/formats/smiley.h:649:76: warning: unused parameter ‘chiralNbrs’ [-Wunused-parameter] 2023-09-12T11:11:45,198 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2023-09-12T11:11:45,199 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:11:45,200 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addAtom(int, bool, int, int, int, int)’: 2023-09-12T11:11:45,201 include/formats/smiley.h:655:22: warning: unused parameter ‘element’ [-Wunused-parameter] 2023-09-12T11:11:45,201 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:11:45,202 | ~~~~^~~~~~~ 2023-09-12T11:11:45,202 include/formats/smiley.h:655:36: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2023-09-12T11:11:45,203 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:11:45,203 | ~~~~~^~~~~~~~ 2023-09-12T11:11:45,204 include/formats/smiley.h:655:50: warning: unused parameter ‘isotope’ [-Wunused-parameter] 2023-09-12T11:11:45,204 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:11:45,205 | ~~~~^~~~~~~ 2023-09-12T11:11:45,206 include/formats/smiley.h:655:63: warning: unused parameter ‘hCount’ [-Wunused-parameter] 2023-09-12T11:11:45,206 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:11:45,207 | ~~~~^~~~~~ 2023-09-12T11:11:45,207 include/formats/smiley.h:655:75: warning: unused parameter ‘charge’ [-Wunused-parameter] 2023-09-12T11:11:45,208 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:11:45,208 | ~~~~^~~~~~ 2023-09-12T11:11:45,209 include/formats/smiley.h:655:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2023-09-12T11:11:45,209 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:11:45,210 | ~~~~^~~~~~~~~ 2023-09-12T11:11:45,211 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addBond(int, int, int, bool, bool)’: 2023-09-12T11:11:45,212 include/formats/smiley.h:659:22: warning: unused parameter ‘source’ [-Wunused-parameter] 2023-09-12T11:11:45,212 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:11:45,213 | ~~~~^~~~~~ 2023-09-12T11:11:45,214 include/formats/smiley.h:659:34: warning: unused parameter ‘target’ [-Wunused-parameter] 2023-09-12T11:11:45,215 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:11:45,215 | ~~~~^~~~~~ 2023-09-12T11:11:45,216 include/formats/smiley.h:659:46: warning: unused parameter ‘order’ [-Wunused-parameter] 2023-09-12T11:11:45,217 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:11:45,217 | ~~~~^~~~~ 2023-09-12T11:11:45,218 include/formats/smiley.h:659:58: warning: unused parameter ‘isUp’ [-Wunused-parameter] 2023-09-12T11:11:45,218 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:11:45,219 | ~~~~~^~~~ 2023-09-12T11:11:45,220 include/formats/smiley.h:659:69: warning: unused parameter ‘isDown’ [-Wunused-parameter] 2023-09-12T11:11:45,220 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:11:45,221 | ~~~~~^~~~~~ 2023-09-12T11:11:45,222 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::operation(int)’: 2023-09-12T11:11:45,222 include/formats/smiley.h:667:24: warning: unused parameter ‘type’ [-Wunused-parameter] 2023-09-12T11:11:45,223 667 | void operation(int type) {} 2023-09-12T11:11:45,224 | ~~~~^~~~ 2023-09-12T11:11:45,224 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addOrganicSubsetAtom(int, bool)’: 2023-09-12T11:11:45,225 include/formats/smiley.h:671:35: warning: unused parameter ‘element’ [-Wunused-parameter] 2023-09-12T11:11:45,226 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2023-09-12T11:11:45,226 | ~~~~^~~~~~~ 2023-09-12T11:11:45,227 include/formats/smiley.h:671:49: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2023-09-12T11:11:45,228 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2023-09-12T11:11:45,228 | ~~~~~^~~~~~~~ 2023-09-12T11:11:45,229 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::atomPrimitive(int, int)’: 2023-09-12T11:11:45,229 include/formats/smiley.h:675:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2023-09-12T11:11:45,230 675 | void atomPrimitive(int type, int value) {} 2023-09-12T11:11:45,230 | ~~~~^~~~ 2023-09-12T11:11:45,231 include/formats/smiley.h:675:38: warning: unused parameter ‘value’ [-Wunused-parameter] 2023-09-12T11:11:45,232 675 | void atomPrimitive(int type, int value) {} 2023-09-12T11:11:45,232 | ~~~~^~~~~ 2023-09-12T11:11:45,233 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::bondPrimitive(int)’: 2023-09-12T11:11:45,234 include/formats/smiley.h:680:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2023-09-12T11:11:45,234 680 | void bondPrimitive(int type) {} 2023-09-12T11:11:45,235 | ~~~~^~~~ 2023-09-12T11:11:45,235 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setPrevious(int)’: 2023-09-12T11:11:45,236 include/formats/smiley.h:685:26: warning: unused parameter ‘index’ [-Wunused-parameter] 2023-09-12T11:11:45,237 685 | void setPrevious(int index) {} 2023-09-12T11:11:45,237 | ~~~~^~~~~ 2023-09-12T11:11:45,238 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::startRingBond(int)’: 2023-09-12T11:11:45,239 include/formats/smiley.h:689:28: warning: unused parameter ‘number’ [-Wunused-parameter] 2023-09-12T11:11:45,239 689 | void startRingBond(int number) {} 2023-09-12T11:11:45,240 | ~~~~^~~~~~ 2023-09-12T11:11:45,241 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::endRingBond(int, int)’: 2023-09-12T11:11:45,241 include/formats/smiley.h:693:26: warning: unused parameter ‘number’ [-Wunused-parameter] 2023-09-12T11:11:45,242 693 | void endRingBond(int number, int index) {} 2023-09-12T11:11:45,243 | ~~~~^~~~~~ 2023-09-12T11:11:45,243 include/formats/smiley.h:693:38: warning: unused parameter ‘index’ [-Wunused-parameter] 2023-09-12T11:11:45,244 693 | void endRingBond(int number, int index) {} 2023-09-12T11:11:45,245 | ~~~~^~~~~ 2023-09-12T11:11:45,333 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::addAtom(int, bool, int, int, int, int)’: 2023-09-12T11:11:45,334 ./src/formats/smileyformat.cpp:58:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2023-09-12T11:11:45,335 58 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) 2023-09-12T11:11:45,335 | ~~~~^~~~~~~~~ 2023-09-12T11:11:45,339 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::setChiral(int, Smiley::Chirality, const std::vector&)’: 2023-09-12T11:11:45,340 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘NotChiral’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,340 153 | switch (chirality) { 2023-09-12T11:11:45,340 | ^ 2023-09-12T11:11:45,341 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH1’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,342 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH2’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,342 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL1’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,343 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL2’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,343 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP1’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,344 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP2’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,344 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP3’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,345 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB1’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,346 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB2’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,346 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB3’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,347 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB4’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,348 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB5’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,348 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB6’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,349 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB7’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,350 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB8’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,351 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB9’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,351 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB10’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,352 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB11’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,353 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB12’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,354 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB13’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,354 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB14’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,355 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB15’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,356 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB16’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,356 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB17’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,357 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB18’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,357 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB19’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,358 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB20’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,359 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH1’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,360 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH2’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,361 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH3’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,361 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH4’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,362 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH5’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,362 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH6’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,363 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH7’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,363 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH8’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,364 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH9’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,364 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH10’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,365 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH11’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,365 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH12’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,366 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH13’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,366 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH14’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,367 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH15’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,368 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH16’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,368 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH17’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,369 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH18’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,370 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH19’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,370 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH20’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,371 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH21’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,371 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH22’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,372 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH23’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,373 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH24’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,373 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH25’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,374 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH26’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,374 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH27’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,375 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH28’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,376 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH29’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,376 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH30’ not handled in switch [-Wswitch] 2023-09-12T11:11:45,411 ./src/formats/smileyformat.cpp: In member function ‘bool OpenBabel::SmileyFormat::AssignNbrAtoms(const std::vector&, OpenBabel::OBAtom*, long unsigned int&, long unsigned int&)’: 2023-09-12T11:11:45,412 ./src/formats/smileyformat.cpp:457:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:11:45,413 457 | aboveId = above ? above->GetId() : OBStereo::ImplicitRef; 2023-09-12T11:11:45,414 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:45,414 ./src/formats/smileyformat.cpp:458:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:11:45,415 458 | belowId = below ? below->GetId() : OBStereo::ImplicitRef; 2023-09-12T11:11:45,415 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:46,076 include/formats/smiley.h: In instantiation of ‘void Smiley::Parser::processStereochemistry() [with Callback = OpenBabel::OpenBabelCallback]’: 2023-09-12T11:11:46,076 include/formats/smiley.h:2707:9: required from ‘void Smiley::Parser::parse(const std::string&) [with Callback = OpenBabel::OpenBabelCallback; std::string = std::__cxx11::basic_string]’ 2023-09-12T11:11:46,077 ./src/formats/smileyformat.cpp:365:19: required from here 2023-09-12T11:11:46,077 include/formats/smiley.h:2642:43: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:11:46,078 2642 | if (m_chiralInfo[i].nbrs.size() != expectedValence && m_exceptions & InvalidChiralValence) 2023-09-12T11:11:46,078 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T11:11:46,709 include/formats/smiley.h: In instantiation of ‘Smiley::Parser::RingBondInfo::RingBondInfo(int, int, bool, bool, bool, std::size_t) [with Callback = OpenBabel::OpenBabelCallback; std::size_t = unsigned int]’: 2023-09-12T11:11:46,709 include/formats/smiley.h:2409:41: required from ‘void Smiley::Parser::processRingBond(int, std::size_t) [with Callback = OpenBabel::OpenBabelCallback; std::size_t = unsigned int]’ 2023-09-12T11:11:46,710 include/formats/smiley.h:2429:11: required from ‘void Smiley::Parser::parseRingBond() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:11:46,711 include/formats/smiley.h:2507:13: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:11:46,712 include/formats/smiley.h:2698:9: required from ‘void Smiley::Parser::parse(const std::string&) [with Callback = OpenBabel::OpenBabelCallback; std::string = std::__cxx11::basic_string]’ 2023-09-12T11:11:46,712 ./src/formats/smileyformat.cpp:365:19: required from here 2023-09-12T11:11:46,713 include/formats/smiley.h:986:14: warning: ‘Smiley::Parser::RingBondInfo::isExplicit’ will be initialized after [-Wreorder] 2023-09-12T11:11:46,714 986 | bool isExplicit; 2023-09-12T11:11:46,714 | ^~~~~~~~~~ 2023-09-12T11:11:46,715 include/formats/smiley.h:981:21: warning: ‘std::size_t Smiley::Parser::RingBondInfo::pos’ [-Wreorder] 2023-09-12T11:11:46,716 981 | std::size_t pos; 2023-09-12T11:11:46,716 | ^~~ 2023-09-12T11:11:46,717 include/formats/smiley.h:974:9: warning: when initialized here [-Wreorder] 2023-09-12T11:11:46,718 974 | RingBondInfo(int number_, int order_, bool isUp_, bool isDown_, 2023-09-12T11:11:46,718 | ^~~~~~~~~~~~ 2023-09-12T11:11:46,790 include/formats/smiley.h: In instantiation of ‘bool Smiley::Parser::parseCharNumber(char, int, int&, bool, bool) [with Callback = OpenBabel::OpenBabelCallback]’: 2023-09-12T11:11:46,790 include/formats/smiley.h:1988:15: required from ‘void Smiley::Parser::parseAtomExpr() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:11:46,791 include/formats/smiley.h:2092:11: required from ‘void Smiley::Parser::parseBracketAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:11:46,792 include/formats/smiley.h:2217:13: required from ‘bool Smiley::Parser::parseAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:11:46,793 include/formats/smiley.h:2495:16: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:11:46,793 include/formats/smiley.h:2698:9: required from ‘void Smiley::Parser::parse(const std::string&) [with Callback = OpenBabel::OpenBabelCallback; std::string = std::__cxx11::basic_string]’ 2023-09-12T11:11:46,794 ./src/formats/smileyformat.cpp:365:19: required from here 2023-09-12T11:11:46,794 include/formats/smiley.h:1774:37: warning: unused parameter ‘noDefault’ [-Wunused-parameter] 2023-09-12T11:11:46,795 1774 | bool firstPrimitive, bool noDefault = false) 2023-09-12T11:11:46,796 | ~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:11:55,029 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/smileyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:55,029 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/smileyformat.o /tmp/ccwofxZf.s 2023-09-12T11:11:55,036 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:11:55,737 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:11:55,738 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:11:55,739 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/smileyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/smileyformat.' 2023-09-12T11:11:55,741 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/stlformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/stlformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:11:55,746 Using built-in specs. 2023-09-12T11:11:55,747 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:11:55,748 Target: arm-linux-gnueabihf 2023-09-12T11:11:55,749 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:11:55,749 Thread model: posix 2023-09-12T11:11:55,750 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:11:55,750 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:11:55,751 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/stlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:11:55,752 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/stlformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase stlformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccfR3oxs.s 2023-09-12T11:11:55,760 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:55,761 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:55,762 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:55,763 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:55,764 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:11:55,764 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:11:55,765 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:11:55,766 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:11:55,766 ignoring duplicate directory "/usr/include/" 2023-09-12T11:11:55,767 as it is a non-system directory that duplicates a system directory 2023-09-12T11:11:55,767 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:11:55,768 #include "..." search starts here: 2023-09-12T11:11:55,768 #include <...> search starts here: 2023-09-12T11:11:55,769 /usr/include/eigen3 2023-09-12T11:11:55,770 include 2023-09-12T11:11:55,770 /usr/include/python3.11 2023-09-12T11:11:55,771 /usr/include/c++/12 2023-09-12T11:11:55,772 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:11:55,772 /usr/include/c++/12/backward 2023-09-12T11:11:55,773 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:11:55,774 /usr/local/include 2023-09-12T11:11:55,775 /usr/include/arm-linux-gnueabihf 2023-09-12T11:11:55,775 /usr/include 2023-09-12T11:11:55,776 End of search list. 2023-09-12T11:11:55,777 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:11:55,778 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:11:55,778 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:11:55,779 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:11:55,779 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:11:57,353 In file included from include/openbabel/atom.h:33, 2023-09-12T11:11:57,353 from include/openbabel/mol.h:43, 2023-09-12T11:11:57,354 from ./src/formats/stlformat.cpp:28: 2023-09-12T11:11:57,355 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:11:57,355 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:11:57,356 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:11:57,356 | ^ 2023-09-12T11:11:57,357 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:11:57,357 37 | # define UNUSED(x) x 2023-09-12T11:11:57,358 | ^ 2023-09-12T11:11:58,122 In file included from include/openbabel/mol.h:52: 2023-09-12T11:11:58,122 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:58,123 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:58,124 862 | {return new OBVibrationData(*this);} 2023-09-12T11:11:58,124 | ^ 2023-09-12T11:11:58,125 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:11:58,126 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:11:58,126 | ^~~~~~~~ 2023-09-12T11:11:58,127 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:58,128 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:58,129 907 | {return new OBDOSData(*this);} 2023-09-12T11:11:58,130 | ^ 2023-09-12T11:11:58,130 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:11:58,131 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:11:58,132 | ^~~~~~~~ 2023-09-12T11:11:58,146 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:58,147 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:58,147 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:11:58,148 | ^ 2023-09-12T11:11:58,149 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:11:58,150 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:11:58,151 | ^~~~~~~~ 2023-09-12T11:11:58,152 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:11:58,153 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:11:58,153 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:11:58,154 | ^ 2023-09-12T11:11:58,155 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:11:58,155 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:11:58,156 | ^~~~~~~~ 2023-09-12T11:11:58,325 In file included from include/openbabel/format.h:22, 2023-09-12T11:11:58,326 from include/openbabel/obconversion.h:37, 2023-09-12T11:11:58,326 from ./src/formats/stlformat.cpp:29: 2023-09-12T11:11:58,327 include/openbabel/plugin.h: At global scope: 2023-09-12T11:11:58,328 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:11:58,328 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:11:58,329 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:58,329 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:11:58,330 from /usr/include/c++/12/vector:66, 2023-09-12T11:11:58,331 from include/openbabel/mol.h:35: 2023-09-12T11:11:58,331 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:11:58,332 131 | struct binary_function 2023-09-12T11:11:58,332 | ^~~~~~~~~~~~~~~ 2023-09-12T11:11:58,524 ./src/formats/stlformat.cpp: In member function ‘virtual int OpenBabel::STLFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:11:58,525 ./src/formats/stlformat.cpp:95:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:11:58,526 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:11:58,527 | ~~~~^ 2023-09-12T11:11:58,527 ./src/formats/stlformat.cpp:95:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:11:58,528 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:11:58,529 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:11:58,542 ./src/formats/stlformat.cpp: In function ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’: 2023-09-12T11:11:58,543 ./src/formats/stlformat.cpp:149:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:11:58,543 149 | for( int i=0 ; i < points.size()-2; i++ ) { 2023-09-12T11:11:58,544 | ~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:12:00,813 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:12:00,813 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:12:00,814 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:12:00,815 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:12:00,816 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:00,901 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::Triangle}; _Tp = OpenBabel::Triangle; _Alloc = std::allocator]’: 2023-09-12T11:12:00,901 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:12:01,018 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:12:01,018 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:01,019 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:144:25: 2023-09-12T11:12:01,019 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:01,020 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:01,021 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:01,021 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:12:01,022 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:01,022 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:145:25: 2023-09-12T11:12:01,023 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:01,024 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:01,025 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:01,025 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::Triangle}; _Tp = OpenBabel::Triangle; _Alloc = std::allocator]’, 2023-09-12T11:12:01,026 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::Triangle; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:01,027 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:152:28: 2023-09-12T11:12:01,027 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:01,028 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:01,029 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:01,029 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::Triangle}; _Tp = OpenBabel::Triangle; _Alloc = std::allocator]’, 2023-09-12T11:12:01,030 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::Triangle; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:01,031 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:155:28: 2023-09-12T11:12:01,031 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:01,032 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:01,032 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:01,380 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/stlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:01,380 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/stlformat.o /tmp/ccfR3oxs.s 2023-09-12T11:12:01,385 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:01,559 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:01,560 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:01,561 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/stlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/stlformat.' 2023-09-12T11:12:01,561 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/svgformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/svgformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:01,565 Using built-in specs. 2023-09-12T11:12:01,566 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:01,567 Target: arm-linux-gnueabihf 2023-09-12T11:12:01,567 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:01,568 Thread model: posix 2023-09-12T11:12:01,569 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:01,569 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:01,570 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/svgformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:01,570 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/svgformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase svgformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccxice1Y.s 2023-09-12T11:12:01,579 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:01,579 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:01,581 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:01,581 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:01,582 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:01,582 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:01,583 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:01,583 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:01,584 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:01,585 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:01,585 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:01,586 #include "..." search starts here: 2023-09-12T11:12:01,586 #include <...> search starts here: 2023-09-12T11:12:01,587 /usr/include/eigen3 2023-09-12T11:12:01,587 include 2023-09-12T11:12:01,588 /usr/include/python3.11 2023-09-12T11:12:01,588 /usr/include/c++/12 2023-09-12T11:12:01,589 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:01,589 /usr/include/c++/12/backward 2023-09-12T11:12:01,590 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:01,590 /usr/local/include 2023-09-12T11:12:01,591 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:01,591 /usr/include 2023-09-12T11:12:01,592 End of search list. 2023-09-12T11:12:01,593 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:01,593 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:01,594 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:01,595 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:01,597 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:03,191 In file included from include/openbabel/atom.h:33, 2023-09-12T11:12:03,191 from include/openbabel/mol.h:43, 2023-09-12T11:12:03,192 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:12:03,192 from ./src/formats/svgformat.cpp:15: 2023-09-12T11:12:03,193 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:03,193 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:03,194 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:03,194 | ^ 2023-09-12T11:12:03,195 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:03,195 37 | # define UNUSED(x) x 2023-09-12T11:12:03,196 | ^ 2023-09-12T11:12:03,962 In file included from include/openbabel/mol.h:52: 2023-09-12T11:12:03,962 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:03,963 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:03,964 862 | {return new OBVibrationData(*this);} 2023-09-12T11:12:03,964 | ^ 2023-09-12T11:12:03,965 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:12:03,965 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:12:03,966 | ^~~~~~~~ 2023-09-12T11:12:03,967 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:03,968 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:03,968 907 | {return new OBDOSData(*this);} 2023-09-12T11:12:03,969 | ^ 2023-09-12T11:12:03,970 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:12:03,970 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:12:03,971 | ^~~~~~~~ 2023-09-12T11:12:03,986 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:03,987 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:03,988 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:12:03,988 | ^ 2023-09-12T11:12:03,989 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:12:03,990 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:12:03,990 | ^~~~~~~~ 2023-09-12T11:12:03,993 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:03,993 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:03,994 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:12:03,995 | ^ 2023-09-12T11:12:03,995 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:12:03,996 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:12:03,997 | ^~~~~~~~ 2023-09-12T11:12:04,167 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:04,167 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:04,168 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:12:04,168 include/openbabel/plugin.h: At global scope: 2023-09-12T11:12:04,169 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:04,169 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:04,170 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:04,170 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:12:04,171 from /usr/include/c++/12/vector:66, 2023-09-12T11:12:04,172 from include/openbabel/mol.h:35: 2023-09-12T11:12:04,172 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:04,173 131 | struct binary_function 2023-09-12T11:12:04,173 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:04,640 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteChemObject(OpenBabel::OBConversion*)’: 2023-09-12T11:12:04,640 ./src/formats/svgformat.cpp:222:42: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:12:04,641 222 | bool nomore = _nmax && (_objects.size()==_nmax); 2023-09-12T11:12:04,642 | ~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:12:04,645 ./src/formats/svgformat.cpp:244:18: warning: unused variable ‘n’ [-Wunused-variable] 2023-09-12T11:12:04,645 244 | unsigned int n=0; 2023-09-12T11:12:04,646 | ^ 2023-09-12T11:12:04,647 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:12:04,647 ./src/formats/svgformat.cpp:269:8: warning: unused variable ‘ret’ [-Wunused-variable] 2023-09-12T11:12:04,648 269 | bool ret = WriteSVG(pConv,_objects); 2023-09-12T11:12:04,649 | ^~~ 2023-09-12T11:12:09,760 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/svgformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:09,761 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/svgformat.o /tmp/ccxice1Y.s 2023-09-12T11:12:09,765 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:10,129 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:10,130 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:10,130 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/svgformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/svgformat.' 2023-09-12T11:12:10,132 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/textformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/textformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:10,136 Using built-in specs. 2023-09-12T11:12:10,137 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:10,137 Target: arm-linux-gnueabihf 2023-09-12T11:12:10,138 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:10,138 Thread model: posix 2023-09-12T11:12:10,139 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:10,140 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:10,140 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/textformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:10,141 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/textformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase textformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccJUB12v.s 2023-09-12T11:12:10,149 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:10,150 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:10,151 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:10,152 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:10,152 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:10,152 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:10,153 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:10,153 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:10,154 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:10,154 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:10,155 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:10,155 #include "..." search starts here: 2023-09-12T11:12:10,156 #include <...> search starts here: 2023-09-12T11:12:10,156 /usr/include/eigen3 2023-09-12T11:12:10,157 include 2023-09-12T11:12:10,157 /usr/include/python3.11 2023-09-12T11:12:10,158 /usr/include/c++/12 2023-09-12T11:12:10,158 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:10,159 /usr/include/c++/12/backward 2023-09-12T11:12:10,159 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:10,160 /usr/local/include 2023-09-12T11:12:10,160 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:10,161 /usr/include 2023-09-12T11:12:10,162 End of search list. 2023-09-12T11:12:10,162 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:10,163 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:10,164 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:10,165 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:10,169 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:11,609 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:11,610 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:11,610 from ./src/formats/textformat.cpp:14: 2023-09-12T11:12:11,611 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:11,612 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:11,613 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:11,613 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:12:11,614 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:12:11,615 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:12:11,615 from /usr/include/c++/12/ios:42, 2023-09-12T11:12:11,616 from /usr/include/c++/12/ostream:38, 2023-09-12T11:12:11,617 from /usr/include/c++/12/iostream:39, 2023-09-12T11:12:11,617 from include/openbabel/obconversion.h:24: 2023-09-12T11:12:11,618 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:11,619 131 | struct binary_function 2023-09-12T11:12:11,620 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:11,758 In file included from include/openbabel/text.h:23, 2023-09-12T11:12:11,759 from ./src/formats/textformat.cpp:15: 2023-09-12T11:12:11,760 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:11,760 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:11,761 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:11,762 | ^ 2023-09-12T11:12:11,762 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:11,763 37 | # define UNUSED(x) x 2023-09-12T11:12:11,763 | ^ 2023-09-12T11:12:13,105 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/textformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:13,105 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/textformat.o /tmp/ccJUB12v.s 2023-09-12T11:12:13,110 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:13,241 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:13,241 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:13,242 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/textformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/textformat.' 2023-09-12T11:12:13,243 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/thermoformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/thermoformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:13,247 Using built-in specs. 2023-09-12T11:12:13,248 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:13,249 Target: arm-linux-gnueabihf 2023-09-12T11:12:13,249 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:13,250 Thread model: posix 2023-09-12T11:12:13,250 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:13,251 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:13,252 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/thermoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:13,252 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/thermoformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase thermoformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccJzJdkz.s 2023-09-12T11:12:13,260 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:13,261 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:13,262 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:13,263 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:13,263 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:13,264 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:13,265 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:13,265 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:13,266 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:13,267 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:13,267 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:13,268 #include "..." search starts here: 2023-09-12T11:12:13,268 #include <...> search starts here: 2023-09-12T11:12:13,269 /usr/include/eigen3 2023-09-12T11:12:13,270 include 2023-09-12T11:12:13,270 /usr/include/python3.11 2023-09-12T11:12:13,271 /usr/include/c++/12 2023-09-12T11:12:13,271 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:13,272 /usr/include/c++/12/backward 2023-09-12T11:12:13,272 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:13,273 /usr/local/include 2023-09-12T11:12:13,273 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:13,274 /usr/include 2023-09-12T11:12:13,275 End of search list. 2023-09-12T11:12:13,275 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:13,276 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:13,277 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:13,278 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:13,283 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:14,986 In file included from include/openbabel/atom.h:33, 2023-09-12T11:12:14,986 from include/openbabel/mol.h:43, 2023-09-12T11:12:14,987 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:12:14,987 from ./src/formats/thermoformat.cpp:19: 2023-09-12T11:12:14,988 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:14,988 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:14,989 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:14,989 | ^ 2023-09-12T11:12:14,990 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:14,990 37 | # define UNUSED(x) x 2023-09-12T11:12:14,991 | ^ 2023-09-12T11:12:15,761 In file included from include/openbabel/mol.h:52: 2023-09-12T11:12:15,761 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:15,762 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:15,762 862 | {return new OBVibrationData(*this);} 2023-09-12T11:12:15,763 | ^ 2023-09-12T11:12:15,763 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:12:15,764 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:12:15,764 | ^~~~~~~~ 2023-09-12T11:12:15,769 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:15,770 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:15,770 907 | {return new OBDOSData(*this);} 2023-09-12T11:12:15,771 | ^ 2023-09-12T11:12:15,772 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:12:15,773 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:12:15,773 | ^~~~~~~~ 2023-09-12T11:12:15,791 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:15,792 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:15,793 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:12:15,793 | ^ 2023-09-12T11:12:15,794 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:12:15,794 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:12:15,795 | ^~~~~~~~ 2023-09-12T11:12:15,801 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:15,801 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:15,802 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:12:15,803 | ^ 2023-09-12T11:12:15,803 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:12:15,804 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:12:15,804 | ^~~~~~~~ 2023-09-12T11:12:15,976 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:15,977 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:15,977 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:12:15,978 include/openbabel/plugin.h: At global scope: 2023-09-12T11:12:15,978 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:15,979 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:15,979 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:15,980 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:12:15,980 from ./src/formats/thermoformat.cpp:17: 2023-09-12T11:12:15,981 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:15,981 131 | struct binary_function 2023-09-12T11:12:15,982 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:16,198 In file included from ./src/formats/thermoformat.cpp:20: 2023-09-12T11:12:16,199 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:16,199 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T11:12:16,200 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2023-09-12T11:12:16,201 | ~~~~~~~~^~~~~~ 2023-09-12T11:12:16,221 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:16,222 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T11:12:16,223 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2023-09-12T11:12:16,224 | ~~~~~~~~^~~~~~ 2023-09-12T11:12:19,759 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/thermoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:19,760 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/thermoformat.o /tmp/ccJzJdkz.s 2023-09-12T11:12:19,764 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:20,005 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:20,006 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:20,006 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/thermoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/thermoformat.' 2023-09-12T11:12:20,007 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/tinkerformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/tinkerformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:20,012 Using built-in specs. 2023-09-12T11:12:20,012 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:20,013 Target: arm-linux-gnueabihf 2023-09-12T11:12:20,013 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:20,014 Thread model: posix 2023-09-12T11:12:20,014 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:20,015 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:20,016 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/tinkerformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:20,016 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/tinkerformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase tinkerformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc0Kryu3.s 2023-09-12T11:12:20,025 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:20,025 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:20,026 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:20,027 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:20,027 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:20,028 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:20,028 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:20,028 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:20,029 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:20,029 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:20,030 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:20,030 #include "..." search starts here: 2023-09-12T11:12:20,031 #include <...> search starts here: 2023-09-12T11:12:20,031 /usr/include/eigen3 2023-09-12T11:12:20,031 include 2023-09-12T11:12:20,032 /usr/include/python3.11 2023-09-12T11:12:20,032 /usr/include/c++/12 2023-09-12T11:12:20,033 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:20,033 /usr/include/c++/12/backward 2023-09-12T11:12:20,033 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:20,034 /usr/local/include 2023-09-12T11:12:20,035 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:20,035 /usr/include 2023-09-12T11:12:20,036 End of search list. 2023-09-12T11:12:20,037 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:20,037 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:20,038 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:20,039 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:20,044 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:21,627 In file included from include/openbabel/atom.h:33, 2023-09-12T11:12:21,628 from include/openbabel/mol.h:43, 2023-09-12T11:12:21,628 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:12:21,629 from ./src/formats/tinkerformat.cpp:17: 2023-09-12T11:12:21,630 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:21,631 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:21,631 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:21,632 | ^ 2023-09-12T11:12:21,632 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:21,633 37 | # define UNUSED(x) x 2023-09-12T11:12:21,634 | ^ 2023-09-12T11:12:22,406 In file included from include/openbabel/mol.h:52: 2023-09-12T11:12:22,407 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:22,407 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:22,408 862 | {return new OBVibrationData(*this);} 2023-09-12T11:12:22,409 | ^ 2023-09-12T11:12:22,410 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:12:22,410 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:12:22,411 | ^~~~~~~~ 2023-09-12T11:12:22,412 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:22,413 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:22,413 907 | {return new OBDOSData(*this);} 2023-09-12T11:12:22,414 | ^ 2023-09-12T11:12:22,414 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:12:22,415 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:12:22,415 | ^~~~~~~~ 2023-09-12T11:12:22,431 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:22,432 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:22,432 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:12:22,433 | ^ 2023-09-12T11:12:22,434 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:12:22,434 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:12:22,435 | ^~~~~~~~ 2023-09-12T11:12:22,438 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:22,439 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:22,440 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:12:22,440 | ^ 2023-09-12T11:12:22,441 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:12:22,442 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:12:22,443 | ^~~~~~~~ 2023-09-12T11:12:22,612 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:22,612 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:22,613 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:12:22,614 include/openbabel/plugin.h: At global scope: 2023-09-12T11:12:22,614 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:22,615 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:22,616 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:22,616 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:12:22,617 from /usr/include/c++/12/vector:66, 2023-09-12T11:12:22,618 from include/openbabel/mol.h:35: 2023-09-12T11:12:22,619 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:22,620 131 | struct binary_function 2023-09-12T11:12:22,620 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:22,896 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T11:12:22,896 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,897 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,897 | ^ 2023-09-12T11:12:22,898 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,898 37 | # define UNUSED(x) x 2023-09-12T11:12:22,899 | ^ 2023-09-12T11:12:22,900 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T11:12:22,900 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,901 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,901 | ^ 2023-09-12T11:12:22,902 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,902 37 | # define UNUSED(x) x 2023-09-12T11:12:22,903 | ^ 2023-09-12T11:12:22,903 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T11:12:22,904 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,905 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,905 | ^ 2023-09-12T11:12:22,906 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,907 37 | # define UNUSED(x) x 2023-09-12T11:12:22,908 | ^ 2023-09-12T11:12:22,908 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T11:12:22,909 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,909 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,910 | ^ 2023-09-12T11:12:22,911 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,912 37 | # define UNUSED(x) x 2023-09-12T11:12:22,912 | ^ 2023-09-12T11:12:22,913 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T11:12:22,914 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,914 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,915 | ^ 2023-09-12T11:12:22,916 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,917 37 | # define UNUSED(x) x 2023-09-12T11:12:22,917 | ^ 2023-09-12T11:12:22,918 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T11:12:22,919 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,919 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,920 | ^ 2023-09-12T11:12:22,921 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,922 37 | # define UNUSED(x) x 2023-09-12T11:12:22,923 | ^ 2023-09-12T11:12:22,923 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T11:12:22,924 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,924 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,925 | ^ 2023-09-12T11:12:22,926 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,926 37 | # define UNUSED(x) x 2023-09-12T11:12:22,927 | ^ 2023-09-12T11:12:22,927 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T11:12:22,928 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:12:22,928 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:12:22,929 | ^ 2023-09-12T11:12:22,929 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:22,930 37 | # define UNUSED(x) x 2023-09-12T11:12:22,931 | ^ 2023-09-12T11:12:22,931 ./src/formats/tinkerformat.cpp: In member function ‘virtual bool OpenBabel::TinkerFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:12:22,932 ./src/formats/tinkerformat.cpp:101:9: warning: unused variable ‘atomicNum’ [-Wunused-variable] 2023-09-12T11:12:22,932 101 | int atomicNum; 2023-09-12T11:12:22,933 | ^~~~~~~~~ 2023-09-12T11:12:22,943 ./src/formats/tinkerformat.cpp: In function ‘int OpenBabel::SetMM3Type(OBAtom*)’: 2023-09-12T11:12:22,944 ./src/formats/tinkerformat.cpp:377:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:12:22,944 377 | if (b->GetHyb() == 2) // S=C 2023-09-12T11:12:22,945 | ^~ 2023-09-12T11:12:22,946 ./src/formats/tinkerformat.cpp:378:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:12:22,946 378 | countNeighborC++; break; 2023-09-12T11:12:22,947 | ^~~~~ 2023-09-12T11:12:22,948 ./src/formats/tinkerformat.cpp:220:17: warning: unused variable ‘c’ [-Wunused-variable] 2023-09-12T11:12:22,949 220 | OBAtom *b, *c; // neighbors 2023-09-12T11:12:22,949 | ^ 2023-09-12T11:12:25,858 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/tinkerformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:25,858 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/tinkerformat.o /tmp/cc0Kryu3.s 2023-09-12T11:12:25,863 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:26,069 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:26,069 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:26,070 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/tinkerformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/tinkerformat.' 2023-09-12T11:12:26,072 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/titleformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/titleformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:26,075 Using built-in specs. 2023-09-12T11:12:26,076 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:26,077 Target: arm-linux-gnueabihf 2023-09-12T11:12:26,077 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:26,077 Thread model: posix 2023-09-12T11:12:26,078 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:26,079 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:26,079 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/titleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:26,080 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/titleformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase titleformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cc706UVZ.s 2023-09-12T11:12:26,089 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:26,089 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:26,091 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:26,091 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:26,091 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:26,092 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:26,092 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:26,092 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:26,093 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:26,093 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:26,094 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:26,094 #include "..." search starts here: 2023-09-12T11:12:26,095 #include <...> search starts here: 2023-09-12T11:12:26,095 /usr/include/eigen3 2023-09-12T11:12:26,096 include 2023-09-12T11:12:26,096 /usr/include/python3.11 2023-09-12T11:12:26,096 /usr/include/c++/12 2023-09-12T11:12:26,097 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:26,097 /usr/include/c++/12/backward 2023-09-12T11:12:26,098 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:26,098 /usr/local/include 2023-09-12T11:12:26,098 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:26,099 /usr/include 2023-09-12T11:12:26,099 End of search list. 2023-09-12T11:12:26,100 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:26,100 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:26,102 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:26,102 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:26,108 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:27,681 In file included from include/openbabel/atom.h:33, 2023-09-12T11:12:27,681 from include/openbabel/mol.h:43, 2023-09-12T11:12:27,682 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:12:27,683 from ./src/formats/titleformat.cpp:19: 2023-09-12T11:12:27,684 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:27,685 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:27,685 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:27,686 | ^ 2023-09-12T11:12:27,687 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:27,687 37 | # define UNUSED(x) x 2023-09-12T11:12:27,688 | ^ 2023-09-12T11:12:28,455 In file included from include/openbabel/mol.h:52: 2023-09-12T11:12:28,455 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:28,456 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:28,457 862 | {return new OBVibrationData(*this);} 2023-09-12T11:12:28,457 | ^ 2023-09-12T11:12:28,458 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:12:28,459 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:12:28,460 | ^~~~~~~~ 2023-09-12T11:12:28,461 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:28,462 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:28,462 907 | {return new OBDOSData(*this);} 2023-09-12T11:12:28,463 | ^ 2023-09-12T11:12:28,464 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:12:28,464 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:12:28,465 | ^~~~~~~~ 2023-09-12T11:12:28,480 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:28,481 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:28,481 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:12:28,482 | ^ 2023-09-12T11:12:28,483 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:12:28,483 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:12:28,484 | ^~~~~~~~ 2023-09-12T11:12:28,487 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:28,487 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:28,488 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:12:28,489 | ^ 2023-09-12T11:12:28,490 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:12:28,490 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:12:28,491 | ^~~~~~~~ 2023-09-12T11:12:28,661 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:28,661 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:28,662 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:12:28,663 include/openbabel/plugin.h: At global scope: 2023-09-12T11:12:28,663 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:28,664 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:28,665 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:28,665 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:12:28,666 from /usr/include/c++/12/vector:66, 2023-09-12T11:12:28,667 from include/openbabel/mol.h:35: 2023-09-12T11:12:28,668 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:28,669 131 | struct binary_function 2023-09-12T11:12:28,669 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:31,050 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/titleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:31,050 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/titleformat.o /tmp/cc706UVZ.s 2023-09-12T11:12:31,055 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:31,183 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:31,183 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:31,184 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/titleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/titleformat.' 2023-09-12T11:12:31,185 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/turbomoleformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/turbomoleformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:31,189 Using built-in specs. 2023-09-12T11:12:31,189 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:31,190 Target: arm-linux-gnueabihf 2023-09-12T11:12:31,191 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:31,191 Thread model: posix 2023-09-12T11:12:31,192 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:31,192 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:31,193 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/turbomoleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:31,194 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/turbomoleformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase turbomoleformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cch7J1xo.s 2023-09-12T11:12:31,202 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:31,203 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:31,204 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:31,204 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:31,205 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:31,205 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:31,206 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:31,206 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:31,207 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:31,208 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:31,208 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:31,209 #include "..." search starts here: 2023-09-12T11:12:31,210 #include <...> search starts here: 2023-09-12T11:12:31,210 /usr/include/eigen3 2023-09-12T11:12:31,211 include 2023-09-12T11:12:31,211 /usr/include/python3.11 2023-09-12T11:12:31,212 /usr/include/c++/12 2023-09-12T11:12:31,213 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:31,213 /usr/include/c++/12/backward 2023-09-12T11:12:31,214 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:31,215 /usr/local/include 2023-09-12T11:12:31,216 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:31,216 /usr/include 2023-09-12T11:12:31,217 End of search list. 2023-09-12T11:12:31,217 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:31,218 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:31,219 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:31,220 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:31,222 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:32,803 In file included from include/openbabel/atom.h:33, 2023-09-12T11:12:32,804 from include/openbabel/mol.h:43, 2023-09-12T11:12:32,804 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:12:32,805 from ./src/formats/turbomoleformat.cpp:18: 2023-09-12T11:12:32,806 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:32,806 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:32,807 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:32,808 | ^ 2023-09-12T11:12:32,809 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:32,809 37 | # define UNUSED(x) x 2023-09-12T11:12:32,810 | ^ 2023-09-12T11:12:33,573 In file included from include/openbabel/mol.h:52: 2023-09-12T11:12:33,573 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:33,574 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:33,575 862 | {return new OBVibrationData(*this);} 2023-09-12T11:12:33,575 | ^ 2023-09-12T11:12:33,576 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:12:33,576 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:12:33,577 | ^~~~~~~~ 2023-09-12T11:12:33,579 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:33,579 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:33,580 907 | {return new OBDOSData(*this);} 2023-09-12T11:12:33,580 | ^ 2023-09-12T11:12:33,581 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:12:33,582 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:12:33,582 | ^~~~~~~~ 2023-09-12T11:12:33,598 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:33,599 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:33,600 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:12:33,601 | ^ 2023-09-12T11:12:33,601 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:12:33,602 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:12:33,603 | ^~~~~~~~ 2023-09-12T11:12:33,606 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:33,607 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:33,608 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:12:33,608 | ^ 2023-09-12T11:12:33,609 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:12:33,610 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:12:33,611 | ^~~~~~~~ 2023-09-12T11:12:33,790 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:33,791 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:33,791 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:12:33,792 include/openbabel/plugin.h: At global scope: 2023-09-12T11:12:33,792 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:33,793 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:33,793 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:33,794 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:12:33,794 from /usr/include/c++/12/vector:66, 2023-09-12T11:12:33,795 from include/openbabel/mol.h:35: 2023-09-12T11:12:33,795 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:33,796 131 | struct binary_function 2023-09-12T11:12:33,796 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:36,402 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/turbomoleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:36,403 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/turbomoleformat.o /tmp/cch7J1xo.s 2023-09-12T11:12:36,408 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:36,553 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:36,554 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:36,555 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/turbomoleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/turbomoleformat.' 2023-09-12T11:12:36,555 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/unichemformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/unichemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:36,559 Using built-in specs. 2023-09-12T11:12:36,560 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:36,561 Target: arm-linux-gnueabihf 2023-09-12T11:12:36,561 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:36,562 Thread model: posix 2023-09-12T11:12:36,563 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:36,563 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:36,564 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/unichemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:36,564 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/unichemformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase unichemformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccAE8a9F.s 2023-09-12T11:12:36,573 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:36,573 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:36,574 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:36,575 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:36,576 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:36,576 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:36,577 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:36,577 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:36,578 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:36,579 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:36,579 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:36,580 #include "..." search starts here: 2023-09-12T11:12:36,580 #include <...> search starts here: 2023-09-12T11:12:36,581 /usr/include/eigen3 2023-09-12T11:12:36,582 include 2023-09-12T11:12:36,582 /usr/include/python3.11 2023-09-12T11:12:36,583 /usr/include/c++/12 2023-09-12T11:12:36,584 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:36,584 /usr/include/c++/12/backward 2023-09-12T11:12:36,585 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:36,585 /usr/local/include 2023-09-12T11:12:36,586 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:36,587 /usr/include 2023-09-12T11:12:36,588 End of search list. 2023-09-12T11:12:36,588 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:36,589 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:36,589 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:36,590 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:36,594 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:38,199 In file included from include/openbabel/atom.h:33, 2023-09-12T11:12:38,200 from include/openbabel/mol.h:43, 2023-09-12T11:12:38,201 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:12:38,201 from ./src/formats/unichemformat.cpp:17: 2023-09-12T11:12:38,202 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:38,202 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:38,203 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:38,203 | ^ 2023-09-12T11:12:38,204 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:38,204 37 | # define UNUSED(x) x 2023-09-12T11:12:38,205 | ^ 2023-09-12T11:12:38,971 In file included from include/openbabel/mol.h:52: 2023-09-12T11:12:38,972 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:38,972 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:38,973 862 | {return new OBVibrationData(*this);} 2023-09-12T11:12:38,974 | ^ 2023-09-12T11:12:38,975 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:12:38,976 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:12:38,978 | ^~~~~~~~ 2023-09-12T11:12:38,979 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:38,980 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:38,980 907 | {return new OBDOSData(*this);} 2023-09-12T11:12:38,981 | ^ 2023-09-12T11:12:38,982 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:12:38,992 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:12:38,996 | ^~~~~~~~ 2023-09-12T11:12:39,000 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:39,122 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:39,123 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:12:39,124 | ^ 2023-09-12T11:12:39,124 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:12:39,125 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:12:39,126 | ^~~~~~~~ 2023-09-12T11:12:39,127 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:39,127 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:39,128 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:12:39,128 | ^ 2023-09-12T11:12:39,129 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:12:39,130 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:12:39,130 | ^~~~~~~~ 2023-09-12T11:12:39,178 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:39,178 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:39,179 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:12:39,180 include/openbabel/plugin.h: At global scope: 2023-09-12T11:12:39,180 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:39,181 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:39,181 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:39,182 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:12:39,183 from /usr/include/c++/12/vector:66, 2023-09-12T11:12:39,183 from include/openbabel/mol.h:35: 2023-09-12T11:12:39,184 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:39,185 131 | struct binary_function 2023-09-12T11:12:39,185 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:41,907 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/unichemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:41,908 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/unichemformat.o /tmp/ccAE8a9F.s 2023-09-12T11:12:41,912 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:42,072 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:42,073 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:42,074 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/unichemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/unichemformat.' 2023-09-12T11:12:42,074 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/vaspformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/vaspformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:42,078 Using built-in specs. 2023-09-12T11:12:42,079 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:42,080 Target: arm-linux-gnueabihf 2023-09-12T11:12:42,080 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:42,081 Thread model: posix 2023-09-12T11:12:42,081 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:42,082 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:42,083 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/vaspformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:42,083 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/vaspformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase vaspformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccyMsJj7.s 2023-09-12T11:12:42,092 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:42,093 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:42,094 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:42,094 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:42,095 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:42,096 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:42,096 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:42,097 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:42,097 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:42,097 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:42,098 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:42,098 #include "..." search starts here: 2023-09-12T11:12:42,099 #include <...> search starts here: 2023-09-12T11:12:42,099 /usr/include/eigen3 2023-09-12T11:12:42,100 include 2023-09-12T11:12:42,100 /usr/include/python3.11 2023-09-12T11:12:42,101 /usr/include/c++/12 2023-09-12T11:12:42,101 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:42,102 /usr/include/c++/12/backward 2023-09-12T11:12:42,102 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:42,102 /usr/local/include 2023-09-12T11:12:42,103 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:42,104 /usr/include 2023-09-12T11:12:42,104 End of search list. 2023-09-12T11:12:42,105 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:42,105 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:42,106 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:42,107 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:42,113 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:12:43,710 In file included from include/openbabel/atom.h:33, 2023-09-12T11:12:43,711 from include/openbabel/mol.h:43, 2023-09-12T11:12:43,711 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:12:43,712 from ./src/formats/vaspformat.cpp:16: 2023-09-12T11:12:43,712 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:12:43,713 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:12:43,714 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:12:43,714 | ^ 2023-09-12T11:12:43,715 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:12:43,716 37 | # define UNUSED(x) x 2023-09-12T11:12:43,716 | ^ 2023-09-12T11:12:44,479 In file included from include/openbabel/mol.h:52: 2023-09-12T11:12:44,480 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:44,480 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:44,481 862 | {return new OBVibrationData(*this);} 2023-09-12T11:12:44,482 | ^ 2023-09-12T11:12:44,482 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:12:44,483 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:12:44,484 | ^~~~~~~~ 2023-09-12T11:12:44,485 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:44,486 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:44,487 907 | {return new OBDOSData(*this);} 2023-09-12T11:12:44,487 | ^ 2023-09-12T11:12:44,488 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:12:44,488 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:12:44,489 | ^~~~~~~~ 2023-09-12T11:12:44,506 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:44,507 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:44,508 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:12:44,508 | ^ 2023-09-12T11:12:44,509 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:12:44,509 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:12:44,510 | ^~~~~~~~ 2023-09-12T11:12:44,513 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:12:44,514 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:12:44,514 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:12:44,515 | ^ 2023-09-12T11:12:44,516 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:12:44,517 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:12:44,517 | ^~~~~~~~ 2023-09-12T11:12:44,693 In file included from include/openbabel/format.h:22, 2023-09-12T11:12:44,694 from include/openbabel/obconversion.h:37, 2023-09-12T11:12:44,695 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:12:44,695 include/openbabel/plugin.h: At global scope: 2023-09-12T11:12:44,696 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:12:44,697 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:12:44,697 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:44,698 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:12:44,699 from /usr/include/c++/12/vector:66, 2023-09-12T11:12:44,699 from include/openbabel/mol.h:35: 2023-09-12T11:12:44,700 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:12:44,700 131 | struct binary_function 2023-09-12T11:12:44,701 | ^~~~~~~~~~~~~~~ 2023-09-12T11:12:45,072 ./src/formats/vaspformat.cpp: In member function ‘virtual int OpenBabel::VASPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:12:45,073 ./src/formats/vaspformat.cpp:111:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:12:45,073 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:12:45,075 | ~~~~^ 2023-09-12T11:12:45,075 ./src/formats/vaspformat.cpp:111:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:12:45,076 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:12:45,076 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:12:45,125 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:12:45,125 ./src/formats/vaspformat.cpp:438:17: warning: unused variable ‘freqnum’ [-Wunused-variable] 2023-09-12T11:12:45,126 438 | int freqnum = atoi(vs[0].c_str()); 2023-09-12T11:12:45,126 | ^~~~~~~ 2023-09-12T11:12:45,131 ./src/formats/vaspformat.cpp:522:35: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = not_equal_to; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:12:45,132 522 | std::bind2nd(std::not_equal_to(), 0.0)); 2023-09-12T11:12:45,132 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:45,133 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T11:12:45,134 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:12:45,134 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:12:45,135 | ^~~~~~~ 2023-09-12T11:12:45,147 ./src/formats/vaspformat.cpp:576:36: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2023-09-12T11:12:45,147 576 | std::bind2nd(std::divides(), max / 100.0)); 2023-09-12T11:12:45,148 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:45,148 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:12:45,149 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:12:45,150 | ^~~~~~~ 2023-09-12T11:12:45,166 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:12:45,167 ./src/formats/vaspformat.cpp:657:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T11:12:45,167 657 | for(int i = 0; i < atoms_sorted.size(); i++) 2023-09-12T11:12:45,168 | ~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:45,180 ./src/formats/vaspformat.cpp:668:34: warning: suggest braces around empty body in an ‘if’ statement [-Wempty-body] 2023-09-12T11:12:45,181 668 | if(atomicNums.size() > 0); 2023-09-12T11:12:45,182 | ^ 2023-09-12T11:12:45,182 ./src/formats/vaspformat.cpp:668:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:12:45,183 668 | if(atomicNums.size() > 0); 2023-09-12T11:12:45,184 | ^~ 2023-09-12T11:12:45,184 ./src/formats/vaspformat.cpp:669:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:12:45,185 669 | atomicNums.rbegin()->second++; 2023-09-12T11:12:45,186 | ^~~~~~~~~~ 2023-09-12T11:12:49,752 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:12:49,753 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::matrix3x3&}; _Tp = OpenBabel::matrix3x3; _Alloc = std::allocator]’: 2023-09-12T11:12:49,754 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:12:49,755 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:12:49,755 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:49,996 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T11:12:49,997 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:12:50,057 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:12:50,057 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:12:52,162 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:12:52,163 ./src/formats/vaspformat.cpp:551:15: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:12:52,164 551 | snprintf(tag, BUFF_SIZE, "%f", pv_eV); 2023-09-12T11:12:52,164 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,165 ./src/formats/vaspformat.cpp:158:25: note: ‘pv_eV’ was declared here 2023-09-12T11:12:52,165 158 | double enthalpy_eV, pv_eV; 2023-09-12T11:12:52,166 | ^~~~~ 2023-09-12T11:12:52,167 ./src/formats/vaspformat.cpp:549:15: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:12:52,168 549 | snprintf(tag, BUFF_SIZE, "%f", enthalpy_eV); 2023-09-12T11:12:52,168 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,169 ./src/formats/vaspformat.cpp:158:12: note: ‘enthalpy_eV’ was declared here 2023-09-12T11:12:52,170 158 | double enthalpy_eV, pv_eV; 2023-09-12T11:12:52,171 | ^~~~~~~~~~~ 2023-09-12T11:12:52,171 ./src/formats/vaspformat.cpp:397:21: warning: ‘fermi’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:12:52,172 397 | dos->SetData(fermi, energies, densities, integration); 2023-09-12T11:12:52,173 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,174 ./src/formats/vaspformat.cpp:379:14: note: ‘fermi’ was declared here 2023-09-12T11:12:52,175 379 | double fermi; 2023-09-12T11:12:52,176 | ^~~~~ 2023-09-12T11:12:52,242 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:12:52,243 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,244 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:391:27: 2023-09-12T11:12:52,244 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,245 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,246 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,246 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:12:52,247 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,248 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:392:28: 2023-09-12T11:12:52,249 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,249 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,250 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,251 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:12:52,251 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,252 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:393:30: 2023-09-12T11:12:52,252 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,253 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,254 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,254 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:12:52,255 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,256 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:441:36: 2023-09-12T11:12:52,257 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,257 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,258 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,259 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:12:52,259 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,260 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:444:36: 2023-09-12T11:12:52,261 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,261 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,262 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,263 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:12:52,263 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,264 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:457:28: 2023-09-12T11:12:52,265 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,266 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,266 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,267 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:12:52,267 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,268 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:482:30: 2023-09-12T11:12:52,268 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,269 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,269 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:52,270 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:12:52,271 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::matrix3x3; _Alloc = std::allocator]’, 2023-09-12T11:12:52,271 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:503:30: 2023-09-12T11:12:52,272 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,273 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:12:52,274 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:12:52,274 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:12:52,275 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:12:52,276 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:570:30: 2023-09-12T11:12:52,276 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:12:52,277 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:12:52,277 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:12:57,602 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:12:57,602 ./src/formats/vaspformat.cpp:752:26: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:12:57,603 752 | if (atom->HasData("move")) { 2023-09-12T11:12:57,604 | ~~~~~~~~~~~~~^~~~~~~~ 2023-09-12T11:12:57,605 ./src/formats/vaspformat.cpp:726:13: note: ‘atom’ was declared here 2023-09-12T11:12:57,605 726 | OBAtom *atom; 2023-09-12T11:12:57,606 | ^~~~ 2023-09-12T11:12:58,724 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/vaspformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:58,725 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/vaspformat.o /tmp/ccyMsJj7.s 2023-09-12T11:12:58,733 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:12:59,732 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:12:59,732 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:12:59,733 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/vaspformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/vaspformat.' 2023-09-12T11:12:59,737 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/viewmolformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/viewmolformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:12:59,741 Using built-in specs. 2023-09-12T11:12:59,742 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:12:59,743 Target: arm-linux-gnueabihf 2023-09-12T11:12:59,744 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:12:59,744 Thread model: posix 2023-09-12T11:12:59,745 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:12:59,746 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:12:59,746 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/viewmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:12:59,747 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/viewmolformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase viewmolformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccj7vvQq.s 2023-09-12T11:12:59,758 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:59,759 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:59,760 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:59,760 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:59,761 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:12:59,761 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:12:59,762 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:12:59,762 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:12:59,763 ignoring duplicate directory "/usr/include/" 2023-09-12T11:12:59,764 as it is a non-system directory that duplicates a system directory 2023-09-12T11:12:59,764 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:12:59,765 #include "..." search starts here: 2023-09-12T11:12:59,766 #include <...> search starts here: 2023-09-12T11:12:59,766 /usr/include/eigen3 2023-09-12T11:12:59,767 include 2023-09-12T11:12:59,768 /usr/include/python3.11 2023-09-12T11:12:59,769 /usr/include/c++/12 2023-09-12T11:12:59,770 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:12:59,770 /usr/include/c++/12/backward 2023-09-12T11:12:59,771 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:12:59,772 /usr/local/include 2023-09-12T11:12:59,772 /usr/include/arm-linux-gnueabihf 2023-09-12T11:12:59,773 /usr/include 2023-09-12T11:12:59,773 End of search list. 2023-09-12T11:12:59,774 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:12:59,775 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:12:59,776 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:12:59,776 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:12:59,781 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:13:01,348 In file included from include/openbabel/atom.h:33, 2023-09-12T11:13:01,348 from include/openbabel/mol.h:43, 2023-09-12T11:13:01,349 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:13:01,350 from ./src/formats/viewmolformat.cpp:17: 2023-09-12T11:13:01,350 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:13:01,351 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:13:01,352 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:13:01,352 | ^ 2023-09-12T11:13:01,353 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:13:01,353 37 | # define UNUSED(x) x 2023-09-12T11:13:01,354 | ^ 2023-09-12T11:13:02,118 In file included from include/openbabel/mol.h:52: 2023-09-12T11:13:02,119 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:02,119 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:02,120 862 | {return new OBVibrationData(*this);} 2023-09-12T11:13:02,120 | ^ 2023-09-12T11:13:02,121 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:13:02,122 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:13:02,122 | ^~~~~~~~ 2023-09-12T11:13:02,123 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:02,124 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:02,125 907 | {return new OBDOSData(*this);} 2023-09-12T11:13:02,125 | ^ 2023-09-12T11:13:02,126 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:13:02,127 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:13:02,128 | ^~~~~~~~ 2023-09-12T11:13:02,142 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:02,143 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:02,144 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:13:02,145 | ^ 2023-09-12T11:13:02,145 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:13:02,146 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:13:02,147 | ^~~~~~~~ 2023-09-12T11:13:02,149 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:02,150 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:02,150 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:13:02,151 | ^ 2023-09-12T11:13:02,152 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:13:02,152 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:13:02,153 | ^~~~~~~~ 2023-09-12T11:13:02,322 In file included from include/openbabel/format.h:22, 2023-09-12T11:13:02,323 from include/openbabel/obconversion.h:37, 2023-09-12T11:13:02,323 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:13:02,324 include/openbabel/plugin.h: At global scope: 2023-09-12T11:13:02,324 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:13:02,325 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:13:02,325 | ^~~~~~~~~~~~~~~ 2023-09-12T11:13:02,326 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:13:02,327 from /usr/include/c++/12/vector:66, 2023-09-12T11:13:02,327 from include/openbabel/mol.h:35: 2023-09-12T11:13:02,328 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:13:02,328 131 | struct binary_function 2023-09-12T11:13:02,329 | ^~~~~~~~~~~~~~~ 2023-09-12T11:13:05,064 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/viewmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:13:05,065 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/viewmolformat.o /tmp/ccj7vvQq.s 2023-09-12T11:13:05,069 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:13:05,223 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:13:05,225 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:13:05,225 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/viewmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/viewmolformat.' 2023-09-12T11:13:05,226 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/xedformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/xedformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:13:05,229 Using built-in specs. 2023-09-12T11:13:05,230 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:13:05,231 Target: arm-linux-gnueabihf 2023-09-12T11:13:05,231 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:13:05,232 Thread model: posix 2023-09-12T11:13:05,232 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:13:05,233 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:13:05,233 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/xedformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:13:05,234 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/xedformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase xedformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccksnZkF.s 2023-09-12T11:13:05,242 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:13:05,243 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:13:05,244 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:13:05,245 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:13:05,245 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:13:05,246 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:13:05,246 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:13:05,247 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:13:05,247 ignoring duplicate directory "/usr/include/" 2023-09-12T11:13:05,248 as it is a non-system directory that duplicates a system directory 2023-09-12T11:13:05,248 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:13:05,249 #include "..." search starts here: 2023-09-12T11:13:05,249 #include <...> search starts here: 2023-09-12T11:13:05,250 /usr/include/eigen3 2023-09-12T11:13:05,251 include 2023-09-12T11:13:05,251 /usr/include/python3.11 2023-09-12T11:13:05,252 /usr/include/c++/12 2023-09-12T11:13:05,252 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:13:05,253 /usr/include/c++/12/backward 2023-09-12T11:13:05,253 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:13:05,254 /usr/local/include 2023-09-12T11:13:05,254 /usr/include/arm-linux-gnueabihf 2023-09-12T11:13:05,255 /usr/include 2023-09-12T11:13:05,255 End of search list. 2023-09-12T11:13:05,255 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:13:05,256 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:13:05,257 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:13:05,257 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:13:05,262 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:13:06,840 In file included from include/openbabel/atom.h:33, 2023-09-12T11:13:06,840 from include/openbabel/mol.h:43, 2023-09-12T11:13:06,841 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:13:06,841 from ./src/formats/xedformat.cpp:17: 2023-09-12T11:13:06,842 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:13:06,843 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:13:06,843 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:13:06,844 | ^ 2023-09-12T11:13:06,844 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:13:06,845 37 | # define UNUSED(x) x 2023-09-12T11:13:06,845 | ^ 2023-09-12T11:13:07,620 In file included from include/openbabel/mol.h:52: 2023-09-12T11:13:07,621 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:07,621 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:07,622 862 | {return new OBVibrationData(*this);} 2023-09-12T11:13:07,623 | ^ 2023-09-12T11:13:07,623 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:13:07,624 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:13:07,625 | ^~~~~~~~ 2023-09-12T11:13:07,626 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:07,627 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:07,628 907 | {return new OBDOSData(*this);} 2023-09-12T11:13:07,628 | ^ 2023-09-12T11:13:07,629 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:13:07,629 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:13:07,630 | ^~~~~~~~ 2023-09-12T11:13:07,646 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:07,647 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:07,647 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:13:07,648 | ^ 2023-09-12T11:13:07,649 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:13:07,649 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:13:07,650 | ^~~~~~~~ 2023-09-12T11:13:07,653 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:07,654 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:07,654 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:13:07,655 | ^ 2023-09-12T11:13:07,655 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:13:07,656 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:13:07,657 | ^~~~~~~~ 2023-09-12T11:13:07,827 In file included from include/openbabel/format.h:22, 2023-09-12T11:13:07,828 from include/openbabel/obconversion.h:37, 2023-09-12T11:13:07,828 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:13:07,829 include/openbabel/plugin.h: At global scope: 2023-09-12T11:13:07,830 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:13:07,830 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:13:07,831 | ^~~~~~~~~~~~~~~ 2023-09-12T11:13:07,832 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:13:07,832 from /usr/include/c++/12/vector:66, 2023-09-12T11:13:07,833 from include/openbabel/mol.h:35: 2023-09-12T11:13:07,833 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:13:07,834 131 | struct binary_function 2023-09-12T11:13:07,835 | ^~~~~~~~~~~~~~~ 2023-09-12T11:13:10,376 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/xedformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:13:10,377 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/xedformat.o /tmp/ccksnZkF.s 2023-09-12T11:13:10,382 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:13:10,521 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:13:10,521 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:13:10,522 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/xedformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/xedformat.' 2023-09-12T11:13:10,523 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/xsfformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/xsfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:13:10,526 Using built-in specs. 2023-09-12T11:13:10,527 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:13:10,528 Target: arm-linux-gnueabihf 2023-09-12T11:13:10,528 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:13:10,529 Thread model: posix 2023-09-12T11:13:10,529 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:13:10,530 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:13:10,530 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/xsfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:13:10,531 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/xsfformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase xsfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/cczcNg9i.s 2023-09-12T11:13:10,540 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:13:10,540 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:13:10,542 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:13:10,542 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:13:10,543 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:13:10,543 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:13:10,544 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:13:10,544 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:13:10,545 ignoring duplicate directory "/usr/include/" 2023-09-12T11:13:10,545 as it is a non-system directory that duplicates a system directory 2023-09-12T11:13:10,545 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:13:10,546 #include "..." search starts here: 2023-09-12T11:13:10,546 #include <...> search starts here: 2023-09-12T11:13:10,547 /usr/include/eigen3 2023-09-12T11:13:10,547 include 2023-09-12T11:13:10,547 /usr/include/python3.11 2023-09-12T11:13:10,548 /usr/include/c++/12 2023-09-12T11:13:10,548 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:13:10,549 /usr/include/c++/12/backward 2023-09-12T11:13:10,549 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:13:10,550 /usr/local/include 2023-09-12T11:13:10,550 /usr/include/arm-linux-gnueabihf 2023-09-12T11:13:10,550 /usr/include 2023-09-12T11:13:10,551 End of search list. 2023-09-12T11:13:10,551 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:13:10,552 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:13:10,553 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:13:10,554 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:13:10,559 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:13:12,133 In file included from include/openbabel/atom.h:33, 2023-09-12T11:13:12,134 from include/openbabel/mol.h:43, 2023-09-12T11:13:12,135 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:13:12,135 from ./src/formats/xsfformat.cpp:16: 2023-09-12T11:13:12,136 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:13:12,137 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:13:12,137 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:13:12,138 | ^ 2023-09-12T11:13:12,138 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:13:12,139 37 | # define UNUSED(x) x 2023-09-12T11:13:12,140 | ^ 2023-09-12T11:13:12,908 In file included from include/openbabel/mol.h:52: 2023-09-12T11:13:12,909 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:12,910 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:12,910 862 | {return new OBVibrationData(*this);} 2023-09-12T11:13:12,911 | ^ 2023-09-12T11:13:12,912 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:13:12,912 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:13:12,913 | ^~~~~~~~ 2023-09-12T11:13:12,914 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:12,915 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:12,916 907 | {return new OBDOSData(*this);} 2023-09-12T11:13:12,917 | ^ 2023-09-12T11:13:12,917 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:13:12,918 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:13:12,919 | ^~~~~~~~ 2023-09-12T11:13:12,934 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:12,935 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:12,936 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:13:12,937 | ^ 2023-09-12T11:13:12,937 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:13:12,939 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:13:12,939 | ^~~~~~~~ 2023-09-12T11:13:12,942 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:13:12,943 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:13:12,944 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:13:12,944 | ^ 2023-09-12T11:13:12,945 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:13:12,946 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:13:12,947 | ^~~~~~~~ 2023-09-12T11:13:13,116 In file included from include/openbabel/format.h:22, 2023-09-12T11:13:13,117 from include/openbabel/obconversion.h:37, 2023-09-12T11:13:13,118 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:13:13,118 include/openbabel/plugin.h: At global scope: 2023-09-12T11:13:13,119 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:13:13,120 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:13:13,120 | ^~~~~~~~~~~~~~~ 2023-09-12T11:13:13,121 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:13:13,122 from /usr/include/c++/12/vector:66, 2023-09-12T11:13:13,122 from include/openbabel/mol.h:35: 2023-09-12T11:13:13,123 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:13:13,124 131 | struct binary_function 2023-09-12T11:13:13,124 | ^~~~~~~~~~~~~~~ 2023-09-12T11:13:15,620 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:13:15,620 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:13:15,621 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:13:15,622 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:13:15,622 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:13:15,830 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:13:15,831 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:13:15,831 inlined from ‘virtual bool OpenBabel::XSFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/xsfformat.cpp:104:36: 2023-09-12T11:13:15,832 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:13:15,832 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:13:15,833 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:13:15,835 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:13:15,836 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-12T11:13:15,837 inlined from ‘virtual bool OpenBabel::XSFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/xsfformat.cpp:145:36: 2023-09-12T11:13:15,837 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-12T11:13:15,838 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:13:15,839 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:13:16,271 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/xsfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:13:16,272 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-311/./src/formats/xsfformat.o /tmp/cczcNg9i.s 2023-09-12T11:13:16,276 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:13:16,468 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/ 2023-09-12T11:13:16,469 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/12/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/12/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2023-09-12T11:13:16,469 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/xsfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/xsfformat.' 2023-09-12T11:13:16,470 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.11 -c ./src/formats/xtcformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/xtcformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:13:16,474 Using built-in specs. 2023-09-12T11:13:16,476 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:13:16,476 Target: arm-linux-gnueabihf 2023-09-12T11:13:16,477 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-12T11:13:16,477 Thread model: posix 2023-09-12T11:13:16,478 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:13:16,478 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:13:16,479 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.11' '-c' '-o' 'build/temp.linux-armv7l-cpython-311/./src/formats/xtcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-311/./src/formats/' 2023-09-12T11:13:16,480 /usr/lib/gcc/arm-linux-gnueabihf/12/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.11 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/xtcformat.cpp -quiet -dumpdir build/temp.linux-armv7l-cpython-311/./src/formats/ -dumpbase xtcformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -g -O2 -O2 -O3 -Wsign-compare -Wformat=1 -Werror=format-security -Wpedantic -Wall -Wextra -std=c++14 -version -fstack-protector-strong -fwrapv -fPIC -o /tmp/ccCdHOkN.s 2023-09-12T11:13:16,489 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:13:16,490 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:13:16,491 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:13:16,492 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:13:16,492 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:13:16,493 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:13:16,494 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:13:16,494 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:13:16,495 ignoring duplicate directory "/usr/include/" 2023-09-12T11:13:16,495 as it is a non-system directory that duplicates a system directory 2023-09-12T11:13:16,496 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:13:16,496 #include "..." search starts here: 2023-09-12T11:13:16,496 #include <...> search starts here: 2023-09-12T11:13:16,497 /usr/include/eigen3 2023-09-12T11:13:16,497 include 2023-09-12T11:13:16,498 /usr/include/python3.11 2023-09-12T11:13:16,498 /usr/include/c++/12 2023-09-12T11:13:16,499 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:13:16,499 /usr/include/c++/12/backward 2023-09-12T11:13:16,499 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:13:16,500 /usr/local/include 2023-09-12T11:13:16,500 /usr/include/arm-linux-gnueabihf 2023-09-12T11:13:16,501 /usr/include 2023-09-12T11:13:16,501 End of search list. 2023-09-12T11:13:16,502 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:13:16,502 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:13:16,503 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:13:16,504 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:13:16,507 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:13:16,848 ./src/formats/xtcformat.cpp:23:10: fatal error: rpc/types.h: No such file or directory 2023-09-12T11:13:16,849 23 | #include 2023-09-12T11:13:16,850 | ^~~~~~~~~~~~~ 2023-09-12T11:13:16,850 compilation terminated. 2023-09-12T11:13:16,863 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-12T11:13:17,009 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-12T11:13:17,022 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-12T11:13:17,022 exec(compile('"'"''"'"''"'"' 2023-09-12T11:13:17,022 # This is -- a caller that pip uses to run setup.py 2023-09-12T11:13:17,022 # 2023-09-12T11:13:17,022 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-12T11:13:17,022 # import from `distutils.core` to work with newer packaging standards. 2023-09-12T11:13:17,022 # - It provides a clear error message when setuptools is not installed. 2023-09-12T11:13:17,022 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-12T11:13:17,022 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-12T11:13:17,022 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-12T11:13:17,022 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-12T11:13:17,022 import os, sys, tokenize 2023-09-12T11:13:17,022 2023-09-12T11:13:17,022 try: 2023-09-12T11:13:17,022 import setuptools 2023-09-12T11:13:17,022 except ImportError as error: 2023-09-12T11:13:17,022 print( 2023-09-12T11:13:17,022 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-12T11:13:17,022 "the build environment.", 2023-09-12T11:13:17,022 file=sys.stderr, 2023-09-12T11:13:17,022 ) 2023-09-12T11:13:17,022 sys.exit(1) 2023-09-12T11:13:17,022 2023-09-12T11:13:17,022 __file__ = %r 2023-09-12T11:13:17,022 sys.argv[0] = __file__ 2023-09-12T11:13:17,022 2023-09-12T11:13:17,022 if os.path.exists(__file__): 2023-09-12T11:13:17,022 filename = __file__ 2023-09-12T11:13:17,022 with tokenize.open(__file__) as f: 2023-09-12T11:13:17,022 setup_py_code = f.read() 2023-09-12T11:13:17,022 else: 2023-09-12T11:13:17,022 filename = "" 2023-09-12T11:13:17,022 setup_py_code = "from setuptools import setup; setup()" 2023-09-12T11:13:17,022 2023-09-12T11:13:17,022 exec(compile(setup_py_code, filename, "exec")) 2023-09-12T11:13:17,022 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-wbntdows/maagbel_aac4441a813c4a88b1e338f5f0615037/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-1p0xjpov[/] 2023-09-12T11:13:17,023 [bold magenta]cwd[/]: /tmp/pip-wheel-wbntdows/maagbel_aac4441a813c4a88b1e338f5f0615037/ 2023-09-12T11:13:17,023 Building wheel for maagbel (setup.py): finished with status 'error' 2023-09-12T11:13:17,025 ERROR: Failed building wheel for maagbel 2023-09-12T11:13:17,026 Running setup.py clean for maagbel 2023-09-12T11:13:17,027 Running command python setup.py clean 2023-09-12T11:13:17,587 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'mail' 2023-09-12T11:13:17,587 warnings.warn(msg) 2023-09-12T11:13:18,132 running clean 2023-09-12T11:13:18,156 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-12T11:13:18,249 'build/lib.linux-armv7l-cpython-311' does not exist -- can't clean it 2023-09-12T11:13:18,249 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-12T11:13:18,250 'build/scripts-3.11' does not exist -- can't clean it 2023-09-12T11:13:18,251 removing 'build' 2023-09-12T11:13:18,357 Failed to build maagbel 2023-09-12T11:13:18,358 ERROR: Failed to build one or more wheels 2023-09-12T11:13:18,360 Exception information: 2023-09-12T11:13:18,360 Traceback (most recent call last): 2023-09-12T11:13:18,360 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-12T11:13:18,360 status = run_func(*args) 2023-09-12T11:13:18,360 ^^^^^^^^^^^^^^^ 2023-09-12T11:13:18,360 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-12T11:13:18,360 return func(self, options, args) 2023-09-12T11:13:18,360 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T11:13:18,360 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-12T11:13:18,360 raise CommandError("Failed to build one or more wheels") 2023-09-12T11:13:18,360 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-12T11:13:18,364 Removed build tracker: '/tmp/pip-build-tracker-xeyiwt3d'