2023-09-12T10:45:25,212 Created temporary directory: /tmp/pip-build-tracker-21zxo5rz 2023-09-12T10:45:25,213 Initialized build tracking at /tmp/pip-build-tracker-21zxo5rz 2023-09-12T10:45:25,214 Created build tracker: /tmp/pip-build-tracker-21zxo5rz 2023-09-12T10:45:25,214 Entered build tracker: /tmp/pip-build-tracker-21zxo5rz 2023-09-12T10:45:25,215 Created temporary directory: /tmp/pip-wheel-v347_ll_ 2023-09-12T10:45:25,218 Created temporary directory: /tmp/pip-ephem-wheel-cache-42099ee2 2023-09-12T10:45:25,240 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-12T10:45:25,244 2 location(s) to search for versions of maagbel: 2023-09-12T10:45:25,244 * https://pypi.org/simple/maagbel/ 2023-09-12T10:45:25,244 * https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:45:25,245 Fetching project page and analyzing links: https://pypi.org/simple/maagbel/ 2023-09-12T10:45:25,246 Getting page https://pypi.org/simple/maagbel/ 2023-09-12T10:45:25,247 Found index url https://pypi.org/simple/ 2023-09-12T10:45:25,492 Fetched page https://pypi.org/simple/maagbel/ as application/vnd.pypi.simple.v1+json 2023-09-12T10:45:25,494 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 2023-09-12T10:45:25,494 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 2023-09-12T10:45:25,495 Fetching project page and analyzing links: https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:45:25,496 Getting page https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:45:25,497 Found index url https://www.piwheels.org/simple/ 2023-09-12T10:45:31,073 Fetched page https://www.piwheels.org/simple/maagbel/ as text/html 2023-09-12T10:45:31,075 Skipping link: not a file: https://www.piwheels.org/simple/maagbel/ 2023-09-12T10:45:31,076 Skipping link: not a file: https://pypi.org/simple/maagbel/ 2023-09-12T10:45:31,114 Given no hashes to check 1 links for project 'maagbel': discarding no candidates 2023-09-12T10:45:31,151 Collecting maagbel==0.1.1 2023-09-12T10:45:31,153 Created temporary directory: /tmp/pip-unpack-uxqyn7vi 2023-09-12T10:45:31,454 Downloading maagbel-0.1.1.tar.gz (1.8 MB) 2023-09-12T10:45:32,922 Added maagbel==0.1.1 from https://files.pythonhosted.org/packages/66/de/8fe70531b8e76dcc8f1208ab3bee0fe940b515b9c5b2bf66832f627331c9/maagbel-0.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-21zxo5rz' 2023-09-12T10:45:32,924 Running setup.py (path:/tmp/pip-wheel-v347_ll_/maagbel_ac2148b3a028460ebbf8680210360358/setup.py) egg_info for package maagbel 2023-09-12T10:45:32,925 Created temporary directory: /tmp/pip-pip-egg-info-kmxg30l9 2023-09-12T10:45:32,926 Preparing metadata (setup.py): started 2023-09-12T10:45:32,927 Running command python setup.py egg_info 2023-09-12T10:45:33,457 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'mail' 2023-09-12T10:45:33,457 warnings.warn(msg) 2023-09-12T10:45:34,004 running egg_info 2023-09-12T10:45:34,006 creating /tmp/pip-pip-egg-info-kmxg30l9/maagbel.egg-info 2023-09-12T10:45:34,030 writing /tmp/pip-pip-egg-info-kmxg30l9/maagbel.egg-info/PKG-INFO 2023-09-12T10:45:34,033 writing dependency_links to /tmp/pip-pip-egg-info-kmxg30l9/maagbel.egg-info/dependency_links.txt 2023-09-12T10:45:34,035 writing top-level names to /tmp/pip-pip-egg-info-kmxg30l9/maagbel.egg-info/top_level.txt 2023-09-12T10:45:34,036 writing manifest file '/tmp/pip-pip-egg-info-kmxg30l9/maagbel.egg-info/SOURCES.txt' 2023-09-12T10:45:34,114 reading manifest file '/tmp/pip-pip-egg-info-kmxg30l9/maagbel.egg-info/SOURCES.txt' 2023-09-12T10:45:34,116 reading manifest template 'MANIFEST.in' 2023-09-12T10:45:34,141 writing manifest file '/tmp/pip-pip-egg-info-kmxg30l9/maagbel.egg-info/SOURCES.txt' 2023-09-12T10:45:34,249 Preparing metadata (setup.py): finished with status 'done' 2023-09-12T10:45:34,253 Source in /tmp/pip-wheel-v347_ll_/maagbel_ac2148b3a028460ebbf8680210360358 has version 0.1.1, which satisfies requirement maagbel==0.1.1 from https://files.pythonhosted.org/packages/66/de/8fe70531b8e76dcc8f1208ab3bee0fe940b515b9c5b2bf66832f627331c9/maagbel-0.1.1.tar.gz 2023-09-12T10:45:34,254 Removed maagbel==0.1.1 from https://files.pythonhosted.org/packages/66/de/8fe70531b8e76dcc8f1208ab3bee0fe940b515b9c5b2bf66832f627331c9/maagbel-0.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-21zxo5rz' 2023-09-12T10:45:34,258 Created temporary directory: /tmp/pip-unpack-3kwy3gq5 2023-09-12T10:45:34,259 Created temporary directory: /tmp/pip-unpack-xxs6zfit 2023-09-12T10:45:34,262 Building wheels for collected packages: maagbel 2023-09-12T10:45:34,265 Created temporary directory: /tmp/pip-wheel-gnlrmcc0 2023-09-12T10:45:34,266 Building wheel for maagbel (setup.py): started 2023-09-12T10:45:34,267 Destination directory: /tmp/pip-wheel-gnlrmcc0 2023-09-12T10:45:34,267 Running command python setup.py bdist_wheel 2023-09-12T10:45:34,780 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'mail' 2023-09-12T10:45:34,781 warnings.warn(msg) 2023-09-12T10:45:35,298 running bdist_wheel 2023-09-12T10:45:35,370 running build 2023-09-12T10:45:35,370 running build_ext 2023-09-12T10:45:35,886 building 'maagbel._cpp' extension 2023-09-12T10:45:35,887 swigging maagbel/cpp.i to maagbel/cpp_wrap.cpp 2023-09-12T10:45:35,888 swig -python -c++ -Iinclude -o maagbel/cpp_wrap.cpp maagbel/cpp.i 2023-09-12T10:45:38,285 include/openbabel/obconversion.h:369: Warning 325: Nested struct not currently supported (StreamState ignored) 2023-09-12T10:45:39,103 include/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored) 2023-09-12T10:45:39,305 include/openbabel/spectrophore.h:571: Warning 312: Nested struct not currently supported (ignored). 2023-09-12T10:45:39,307 include/openbabel/spectrophore.h:578: Warning 312: Nested struct not currently supported (ignored). 2023-09-12T10:46:00,695 creating build 2023-09-12T10:46:00,695 creating build/temp.linux-armv7l-cpython-311 2023-09-12T10:46:00,696 creating build/temp.linux-armv7l-cpython-311/src 2023-09-12T10:46:00,698 creating build/temp.linux-armv7l-cpython-311/src/charges 2023-09-12T10:46:00,699 creating build/temp.linux-armv7l-cpython-311/src/depict 2023-09-12T10:46:00,699 creating build/temp.linux-armv7l-cpython-311/src/descriptors 2023-09-12T10:46:00,700 creating build/temp.linux-armv7l-cpython-311/src/fingerprints 2023-09-12T10:46:00,701 creating build/temp.linux-armv7l-cpython-311/src/forcefields 2023-09-12T10:46:00,702 creating build/temp.linux-armv7l-cpython-311/src/formats 2023-09-12T10:46:00,706 creating build/temp.linux-armv7l-cpython-311/src/math 2023-09-12T10:46:00,707 creating build/temp.linux-armv7l-cpython-311/src/ops 2023-09-12T10:46:00,708 creating build/temp.linux-armv7l-cpython-311/src/stereo 2023-09-12T10:46:00,709 creating build/temp.linux-armv7l-cpython-311/maagbel 2023-09-12T10:46:00,710 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 2023-09-12T10:46:00,715 Using built-in specs. 2023-09-12T10:46:00,717 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:00,717 Target: arm-linux-gnueabihf 2023-09-12T10:46:00,718 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 2023-09-12T10:46:00,719 Thread model: posix 2023-09-12T10:46:00,719 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:00,720 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:00,720 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/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/' 2023-09-12T10:46:00,721 /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/cctRLKak.s 2023-09-12T10:46:00,731 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:00,731 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:00,732 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:00,733 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:00,733 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:00,734 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:00,735 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:00,735 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:00,736 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:00,736 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:00,737 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:00,738 #include "..." search starts here: 2023-09-12T10:46:00,738 #include <...> search starts here: 2023-09-12T10:46:00,739 /usr/include/eigen3 2023-09-12T10:46:00,739 include 2023-09-12T10:46:00,740 /usr/include/python3.11 2023-09-12T10:46:00,740 /usr/include/c++/12 2023-09-12T10:46:00,741 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:00,741 /usr/include/c++/12/backward 2023-09-12T10:46:00,742 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:00,743 /usr/local/include 2023-09-12T10:46:00,743 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:00,744 /usr/include 2023-09-12T10:46:00,745 End of search list. 2023-09-12T10:46:00,745 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:00,746 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:00,748 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:00,748 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:00,752 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:03,008 In file included from include/openbabel/atom.h:33, 2023-09-12T10:46:03,009 from include/openbabel/mol.h:43, 2023-09-12T10:46:03,010 from ./src/aggregate.cpp:20: 2023-09-12T10:46:03,010 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:46:03,011 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:46:03,011 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:46:03,012 | ^ 2023-09-12T10:46:03,012 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:03,013 37 | # define UNUSED(x) x 2023-09-12T10:46:03,014 | ^ 2023-09-12T10:46:03,785 In file included from include/openbabel/mol.h:52: 2023-09-12T10:46:03,785 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:03,786 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:03,786 862 | {return new OBVibrationData(*this);} 2023-09-12T10:46:03,787 | ^ 2023-09-12T10:46:03,787 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:46:03,788 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:46:03,789 | ^~~~~~~~ 2023-09-12T10:46:03,790 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:03,791 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:03,792 907 | {return new OBDOSData(*this);} 2023-09-12T10:46:03,793 | ^ 2023-09-12T10:46:03,793 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:46:03,794 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:46:03,795 | ^~~~~~~~ 2023-09-12T10:46:03,810 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:03,811 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:03,811 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:46:03,812 | ^ 2023-09-12T10:46:03,813 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:46:03,813 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:46:03,814 | ^~~~~~~~ 2023-09-12T10:46:03,817 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:03,818 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:03,818 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:46:03,819 | ^ 2023-09-12T10:46:03,820 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:46:03,820 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:46:03,821 | ^~~~~~~~ 2023-09-12T10:46:04,035 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:46:04,036 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:46:04,036 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:46:04,037 | ^ 2023-09-12T10:46:04,037 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:04,038 37 | # define UNUSED(x) x 2023-09-12T10:46:04,038 | ^ 2023-09-12T10:46:04,039 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:46:04,039 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:46:04,040 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:46:04,041 | ^ 2023-09-12T10:46:04,042 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:04,042 37 | # define UNUSED(x) x 2023-09-12T10:46:04,043 | ^ 2023-09-12T10:46:04,374 ./src/aggregate.cpp: In member function ‘float OpenBabel::OBAggregate::MinVDWDist(bool, double)’: 2023-09-12T10:46:04,374 ./src/aggregate.cpp:151:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:46:04,375 151 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2023-09-12T10:46:04,376 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:46:04,376 ./src/aggregate.cpp:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:46:04,377 156 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2023-09-12T10:46:04,378 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:46:04,384 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’: 2023-09-12T10:46:04,385 ./src/aggregate.cpp:245:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:46:04,386 245 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2023-09-12T10:46:04,386 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:46:04,406 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::FindAllConnections(bool)’: 2023-09-12T10:46:04,406 ./src/aggregate.cpp:316:20: warning: unused variable ‘a’ [-Wunused-variable] 2023-09-12T10:46:04,407 316 | OBAtom *atom, *a; 2023-09-12T10:46:04,407 | ^ 2023-09-12T10:46:04,428 ./src/aggregate.cpp: In member function ‘std::string OpenBabel::OBAggregate::GetConnections()’: 2023-09-12T10:46:04,429 ./src/aggregate.cpp:558:13: warning: unused variable ‘id’ [-Wunused-variable] 2023-09-12T10:46:04,430 558 | int id = -1; 2023-09-12T10:46:04,431 | ^~ 2023-09-12T10:46:04,431 ./src/aggregate.cpp:559:13: warning: unused variable ‘elements’ [-Wunused-variable] 2023-09-12T10:46:04,432 559 | int elements = 0; 2023-09-12T10:46:04,432 | ^~~~~~~~ 2023-09-12T10:46:04,434 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::PrintConnections()’: 2023-09-12T10:46:04,434 ./src/aggregate.cpp:584:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:46:04,435 584 | if ( atom->GetIdx() != id+1 ){ 2023-09-12T10:46:04,435 | ~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T10:46:04,460 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::AddToTag(int, int)’: 2023-09-12T10:46:04,461 ./src/aggregate.cpp:772:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:46:04,461 772 | if (tag >= _molTags.size() || tag<0){ 2023-09-12T10:46:04,462 | ~~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T10:46:09,597 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:46:09,598 from include/openbabel/mol.h:35: 2023-09-12T10:46:09,598 /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]’: 2023-09-12T10:46:09,599 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:46:09,599 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:46:09,600 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:46:10,693 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:46:10,693 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, 2023-09-12T10:46:10,694 inlined from ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’ at ./src/aggregate.cpp:244:29: 2023-09-12T10:46:10,695 /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 2023-09-12T10:46:10,695 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:46:10,696 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:46:10,697 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:46:10,697 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, 2023-09-12T10:46:10,698 inlined from ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’ at ./src/aggregate.cpp:246:31: 2023-09-12T10:46:10,699 /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 2023-09-12T10:46:10,699 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:46:10,700 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:46:12,342 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:12,343 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/cctRLKak.s 2023-09-12T10:46:12,349 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:46:12,885 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/ 2023-09-12T10:46:12,885 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/ 2023-09-12T10:46:12,886 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:46:12,888 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 2023-09-12T10:46:12,892 Using built-in specs. 2023-09-12T10:46:12,893 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:12,894 Target: arm-linux-gnueabihf 2023-09-12T10:46:12,894 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 2023-09-12T10:46:12,895 Thread model: posix 2023-09-12T10:46:12,895 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:12,896 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:12,896 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/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/' 2023-09-12T10:46:12,897 /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/ccPmi9ZZ.s 2023-09-12T10:46:12,906 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:12,906 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:12,907 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:12,908 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:12,908 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:12,909 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:12,909 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:12,910 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:12,910 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:12,910 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:12,911 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:12,911 #include "..." search starts here: 2023-09-12T10:46:12,912 #include <...> search starts here: 2023-09-12T10:46:12,912 /usr/include/eigen3 2023-09-12T10:46:12,913 include 2023-09-12T10:46:12,914 /usr/include/python3.11 2023-09-12T10:46:12,914 /usr/include/c++/12 2023-09-12T10:46:12,915 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:12,915 /usr/include/c++/12/backward 2023-09-12T10:46:12,916 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:12,917 /usr/local/include 2023-09-12T10:46:12,917 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:12,918 /usr/include 2023-09-12T10:46:12,919 End of search list. 2023-09-12T10:46:12,919 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:12,920 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:12,921 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:12,922 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:12,928 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:14,664 In file included from include/openbabel/atom.h:33, 2023-09-12T10:46:14,665 from include/openbabel/mol.h:43, 2023-09-12T10:46:14,666 from include/openbabel/alias.h:20, 2023-09-12T10:46:14,666 from ./src/alias.cpp:17: 2023-09-12T10:46:14,667 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:46:14,668 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:46:14,668 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:46:14,669 | ^ 2023-09-12T10:46:14,670 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:14,671 37 | # define UNUSED(x) x 2023-09-12T10:46:14,671 | ^ 2023-09-12T10:46:15,431 In file included from include/openbabel/mol.h:52: 2023-09-12T10:46:15,432 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:15,433 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:15,433 862 | {return new OBVibrationData(*this);} 2023-09-12T10:46:15,434 | ^ 2023-09-12T10:46:15,434 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:46:15,435 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:46:15,436 | ^~~~~~~~ 2023-09-12T10:46:15,437 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:15,438 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:15,439 907 | {return new OBDOSData(*this);} 2023-09-12T10:46:15,439 | ^ 2023-09-12T10:46:15,440 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:46:15,440 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:46:15,441 | ^~~~~~~~ 2023-09-12T10:46:15,458 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:15,458 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:15,459 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:46:15,459 | ^ 2023-09-12T10:46:15,460 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:46:15,461 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:46:15,462 | ^~~~~~~~ 2023-09-12T10:46:15,465 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:15,466 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:15,467 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:46:15,467 | ^ 2023-09-12T10:46:15,468 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:46:15,469 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:46:15,469 | ^~~~~~~~ 2023-09-12T10:46:15,679 In file included from include/openbabel/format.h:22, 2023-09-12T10:46:15,680 from include/openbabel/obconversion.h:37, 2023-09-12T10:46:15,681 from ./src/alias.cpp:18: 2023-09-12T10:46:15,681 include/openbabel/plugin.h: At global scope: 2023-09-12T10:46:15,682 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:46:15,683 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:46:15,684 | ^~~~~~~~~~~~~~~ 2023-09-12T10:46:15,684 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:46:15,685 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:46:15,685 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:46:15,686 from /usr/include/c++/12/ios:42, 2023-09-12T10:46:15,686 from /usr/include/c++/12/istream:38, 2023-09-12T10:46:15,687 from /usr/include/c++/12/sstream:38, 2023-09-12T10:46:15,687 from ./src/alias.cpp:15: 2023-09-12T10:46:15,688 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:46:15,688 131 | struct binary_function 2023-09-12T10:46:15,689 | ^~~~~~~~~~~~~~~ 2023-09-12T10:46:20,812 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/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/' 2023-09-12T10:46:20,813 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/ccPmi9ZZ.s 2023-09-12T10:46:20,817 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:46:21,166 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/ 2023-09-12T10:46:21,166 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/ 2023-09-12T10:46:21,167 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/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.' 2023-09-12T10:46:21,168 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 2023-09-12T10:46:21,173 Using built-in specs. 2023-09-12T10:46:21,174 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:21,175 Target: arm-linux-gnueabihf 2023-09-12T10:46:21,175 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 2023-09-12T10:46:21,176 Thread model: posix 2023-09-12T10:46:21,177 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:21,177 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:21,178 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:21,178 /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/ccMvoRnY.s 2023-09-12T10:46:21,187 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:21,187 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:21,188 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:21,189 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:21,190 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:21,190 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:21,191 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:21,192 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:21,192 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:21,193 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:21,194 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:21,194 #include "..." search starts here: 2023-09-12T10:46:21,195 #include <...> search starts here: 2023-09-12T10:46:21,195 /usr/include/eigen3 2023-09-12T10:46:21,196 include 2023-09-12T10:46:21,196 /usr/include/python3.11 2023-09-12T10:46:21,197 /usr/include/c++/12 2023-09-12T10:46:21,197 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:21,198 /usr/include/c++/12/backward 2023-09-12T10:46:21,199 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:21,199 /usr/local/include 2023-09-12T10:46:21,200 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:21,201 /usr/include 2023-09-12T10:46:21,201 End of search list. 2023-09-12T10:46:21,202 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:21,203 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 2023-09-12T10:46:21,204 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:21,205 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:21,205 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:22,674 In file included from include/openbabel/atom.h:33, 2023-09-12T10:46:22,675 from ./src/atom.cpp:22: 2023-09-12T10:46:22,675 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:46:22,676 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:46:22,676 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:46:22,677 | ^ 2023-09-12T10:46:22,678 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:22,678 37 | # define UNUSED(x) x 2023-09-12T10:46:22,679 | ^ 2023-09-12T10:46:23,523 In file included from include/openbabel/mol.h:52, 2023-09-12T10:46:23,523 from include/openbabel/isomorphism.h:27, 2023-09-12T10:46:23,524 from include/openbabel/stereo/stereo.h:28, 2023-09-12T10:46:23,525 from ./src/atom.cpp:23: 2023-09-12T10:46:23,525 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:23,526 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:23,526 862 | {return new OBVibrationData(*this);} 2023-09-12T10:46:23,527 | ^ 2023-09-12T10:46:23,528 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:46:23,528 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:46:23,529 | ^~~~~~~~ 2023-09-12T10:46:23,529 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:23,530 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:23,531 907 | {return new OBDOSData(*this);} 2023-09-12T10:46:23,532 | ^ 2023-09-12T10:46:23,532 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:46:23,533 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:46:23,534 | ^~~~~~~~ 2023-09-12T10:46:23,547 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:23,548 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:23,549 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:46:23,550 | ^ 2023-09-12T10:46:23,550 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:46:23,551 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:46:23,552 | ^~~~~~~~ 2023-09-12T10:46:23,554 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:23,555 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:23,555 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:46:23,556 | ^ 2023-09-12T10:46:23,556 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:46:23,557 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:46:23,557 | ^~~~~~~~ 2023-09-12T10:46:23,922 ./src/atom.cpp: In member function ‘int OpenBabel::OBAtom::HighestBondOrder()’: 2023-09-12T10:46:23,923 ./src/atom.cpp:302:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:46:23,924 302 | if(bond->GetBO() > highest) 2023-09-12T10:46:23,924 | ~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T10:46:30,375 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/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/' 2023-09-12T10:46:30,375 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/ccMvoRnY.s 2023-09-12T10:46:30,382 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:46:30,833 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/ 2023-09-12T10:46:30,833 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/ 2023-09-12T10:46:30,834 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/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.' 2023-09-12T10:46:30,836 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 2023-09-12T10:46:30,841 Using built-in specs. 2023-09-12T10:46:30,842 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:30,843 Target: arm-linux-gnueabihf 2023-09-12T10:46:30,844 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 2023-09-12T10:46:30,844 Thread model: posix 2023-09-12T10:46:30,845 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:30,845 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:30,846 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:30,846 /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/ccwve96i.s 2023-09-12T10:46:30,854 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:30,855 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:30,856 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:30,857 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:30,858 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:30,858 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:30,859 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:30,859 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:30,860 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:30,860 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:30,861 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:30,862 #include "..." search starts here: 2023-09-12T10:46:30,862 #include <...> search starts here: 2023-09-12T10:46:30,863 /usr/include/eigen3 2023-09-12T10:46:30,864 include 2023-09-12T10:46:30,864 /usr/include/python3.11 2023-09-12T10:46:30,865 /usr/include/c++/12 2023-09-12T10:46:30,865 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:30,866 /usr/include/c++/12/backward 2023-09-12T10:46:30,867 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:30,868 /usr/local/include 2023-09-12T10:46:30,868 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:30,869 /usr/include 2023-09-12T10:46:30,869 End of search list. 2023-09-12T10:46:30,870 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:30,870 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:30,871 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:30,872 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:30,876 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:32,224 In file included from ./src/base.cpp:21: 2023-09-12T10:46:32,225 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:46:32,226 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:46:32,226 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:46:32,227 | ^ 2023-09-12T10:46:32,227 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:32,228 37 | # define UNUSED(x) x 2023-09-12T10:46:32,229 | ^ 2023-09-12T10:46:33,446 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:33,447 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/ccwve96i.s 2023-09-12T10:46:33,452 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:46:33,556 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/ 2023-09-12T10:46:33,557 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/ 2023-09-12T10:46:33,557 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:46:33,558 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 2023-09-12T10:46:33,562 Using built-in specs. 2023-09-12T10:46:33,563 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:33,564 Target: arm-linux-gnueabihf 2023-09-12T10:46:33,564 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 2023-09-12T10:46:33,565 Thread model: posix 2023-09-12T10:46:33,566 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:33,566 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:33,567 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:33,567 /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/cc51xJyX.s 2023-09-12T10:46:33,575 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:33,576 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 2023-09-12T10:46:33,577 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:33,578 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:33,579 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:33,579 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:33,580 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:33,580 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:33,581 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:33,582 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:33,582 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:33,583 #include "..." search starts here: 2023-09-12T10:46:33,583 #include <...> search starts here: 2023-09-12T10:46:33,584 /usr/include/eigen3 2023-09-12T10:46:33,585 include 2023-09-12T10:46:33,585 /usr/include/python3.11 2023-09-12T10:46:33,586 /usr/include/c++/12 2023-09-12T10:46:33,587 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:33,587 /usr/include/c++/12/backward 2023-09-12T10:46:33,588 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:33,589 /usr/local/include 2023-09-12T10:46:33,589 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:33,590 /usr/include 2023-09-12T10:46:33,591 End of search list. 2023-09-12T10:46:33,591 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:33,592 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:33,592 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:33,593 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:33,594 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:37,853 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:37,854 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/cc51xJyX.s 2023-09-12T10:46:37,859 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:46:38,096 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/ 2023-09-12T10:46:38,097 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/ 2023-09-12T10:46:38,097 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:46:38,098 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 2023-09-12T10:46:38,103 Using built-in specs. 2023-09-12T10:46:38,104 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:38,105 Target: arm-linux-gnueabihf 2023-09-12T10:46:38,105 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 2023-09-12T10:46:38,106 Thread model: posix 2023-09-12T10:46:38,106 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:38,107 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:38,107 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:38,108 /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/ccBk305s.s 2023-09-12T10:46:38,117 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:38,117 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:38,118 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:38,119 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:38,120 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:38,120 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:38,121 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:38,121 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:38,122 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:38,123 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:38,123 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:38,124 #include "..." search starts here: 2023-09-12T10:46:38,124 #include <...> search starts here: 2023-09-12T10:46:38,125 /usr/include/eigen3 2023-09-12T10:46:38,126 include 2023-09-12T10:46:38,126 /usr/include/python3.11 2023-09-12T10:46:38,127 /usr/include/c++/12 2023-09-12T10:46:38,127 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:38,128 /usr/include/c++/12/backward 2023-09-12T10:46:38,128 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:38,129 /usr/local/include 2023-09-12T10:46:38,129 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:38,130 /usr/include 2023-09-12T10:46:38,130 End of search list. 2023-09-12T10:46:38,131 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:38,132 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:38,133 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:38,133 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:38,134 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:39,588 In file included from include/openbabel/bond.h:31, 2023-09-12T10:46:39,588 from ./src/bond.cpp:21: 2023-09-12T10:46:39,589 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:46:39,590 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:46:39,591 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:46:39,591 | ^ 2023-09-12T10:46:39,592 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:39,592 37 | # define UNUSED(x) x 2023-09-12T10:46:39,593 | ^ 2023-09-12T10:46:40,433 In file included from include/openbabel/mol.h:52, 2023-09-12T10:46:40,434 from ./src/bond.cpp:22: 2023-09-12T10:46:40,434 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:40,435 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:40,435 862 | {return new OBVibrationData(*this);} 2023-09-12T10:46:40,436 | ^ 2023-09-12T10:46:40,436 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:46:40,437 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:46:40,438 | ^~~~~~~~ 2023-09-12T10:46:40,438 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:40,439 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:40,440 907 | {return new OBDOSData(*this);} 2023-09-12T10:46:40,440 | ^ 2023-09-12T10:46:40,441 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:46:40,442 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:46:40,443 | ^~~~~~~~ 2023-09-12T10:46:40,457 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:40,458 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:40,459 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:46:40,460 | ^ 2023-09-12T10:46:40,460 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:46:40,461 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:46:40,462 | ^~~~~~~~ 2023-09-12T10:46:40,464 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:40,464 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:40,465 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:46:40,466 | ^ 2023-09-12T10:46:40,467 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:46:40,468 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:46:40,468 | ^~~~~~~~ 2023-09-12T10:46:43,528 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/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/' 2023-09-12T10:46:43,529 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/ccBk305s.s 2023-09-12T10:46:43,533 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:46:43,715 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/ 2023-09-12T10:46:43,716 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/ 2023-09-12T10:46:43,717 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/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.' 2023-09-12T10:46:43,718 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 2023-09-12T10:46:43,722 Using built-in specs. 2023-09-12T10:46:43,723 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:43,723 Target: arm-linux-gnueabihf 2023-09-12T10:46:43,724 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 2023-09-12T10:46:43,725 Thread model: posix 2023-09-12T10:46:43,725 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:43,726 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:43,726 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:43,727 /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/ccOgu22L.s 2023-09-12T10:46:43,735 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:43,736 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:43,737 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:43,738 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:43,738 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:43,739 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:43,739 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:43,740 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:43,740 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:43,741 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:43,741 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:43,742 #include "..." search starts here: 2023-09-12T10:46:43,743 #include <...> search starts here: 2023-09-12T10:46:43,743 /usr/include/eigen3 2023-09-12T10:46:43,744 include 2023-09-12T10:46:43,744 /usr/include/python3.11 2023-09-12T10:46:43,745 /usr/include/c++/12 2023-09-12T10:46:43,746 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:43,746 /usr/include/c++/12/backward 2023-09-12T10:46:43,747 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:43,747 /usr/local/include 2023-09-12T10:46:43,748 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:43,748 /usr/include 2023-09-12T10:46:43,749 End of search list. 2023-09-12T10:46:43,749 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:43,750 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 2023-09-12T10:46:43,751 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:43,752 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:43,753 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:45,311 In file included from include/openbabel/atom.h:33, 2023-09-12T10:46:45,311 from include/openbabel/mol.h:43, 2023-09-12T10:46:45,312 from ./src/bondtyper.cpp:20: 2023-09-12T10:46:45,313 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:46:45,314 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:46:45,315 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:46:45,315 | ^ 2023-09-12T10:46:45,316 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:45,316 37 | # define UNUSED(x) x 2023-09-12T10:46:45,317 | ^ 2023-09-12T10:46:46,078 In file included from include/openbabel/mol.h:52: 2023-09-12T10:46:46,079 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:46,079 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:46,080 862 | {return new OBVibrationData(*this);} 2023-09-12T10:46:46,081 | ^ 2023-09-12T10:46:46,081 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:46:46,082 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:46:46,082 | ^~~~~~~~ 2023-09-12T10:46:46,083 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:46,084 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:46,085 907 | {return new OBDOSData(*this);} 2023-09-12T10:46:46,086 | ^ 2023-09-12T10:46:46,086 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:46:46,087 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:46:46,088 | ^~~~~~~~ 2023-09-12T10:46:46,102 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:46,103 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:46,104 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:46:46,105 | ^ 2023-09-12T10:46:46,105 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:46:46,106 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:46:46,107 | ^~~~~~~~ 2023-09-12T10:46:46,109 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:46,109 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:46,110 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:46:46,111 | ^ 2023-09-12T10:46:46,112 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:46:46,113 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:46:46,113 | ^~~~~~~~ 2023-09-12T10:46:49,582 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:49,583 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/ccOgu22L.s 2023-09-12T10:46:49,587 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:46:49,804 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/ 2023-09-12T10:46:49,804 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/ 2023-09-12T10:46:49,805 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:46:49,806 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 2023-09-12T10:46:49,810 Using built-in specs. 2023-09-12T10:46:49,811 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:46:49,812 Target: arm-linux-gnueabihf 2023-09-12T10:46:49,812 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 2023-09-12T10:46:49,813 Thread model: posix 2023-09-12T10:46:49,813 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:46:49,814 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:46:49,815 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:46:49,815 /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/ccaWaNHx.s 2023-09-12T10:46:49,825 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:49,825 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:49,826 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:49,827 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:49,827 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:46:49,828 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:46:49,828 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:46:49,829 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:46:49,829 ignoring duplicate directory "/usr/include/" 2023-09-12T10:46:49,830 as it is a non-system directory that duplicates a system directory 2023-09-12T10:46:49,830 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:46:49,831 #include "..." search starts here: 2023-09-12T10:46:49,832 #include <...> search starts here: 2023-09-12T10:46:49,832 /usr/include/eigen3 2023-09-12T10:46:49,833 include 2023-09-12T10:46:49,834 /usr/include/python3.11 2023-09-12T10:46:49,834 /usr/include/c++/12 2023-09-12T10:46:49,835 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:46:49,836 /usr/include/c++/12/backward 2023-09-12T10:46:49,836 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:46:49,837 /usr/local/include 2023-09-12T10:46:49,837 /usr/include/arm-linux-gnueabihf 2023-09-12T10:46:49,838 /usr/include 2023-09-12T10:46:49,838 End of search list. 2023-09-12T10:46:49,839 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:46:49,839 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:46:49,840 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:46:49,841 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:46:49,850 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:46:50,569 ./src/builder.cpp:188:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:46:50,569 188 | // \ \ 2023-09-12T10:46:50,570 | ^ 2023-09-12T10:46:50,571 ./src/builder.cpp:190:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:46:50,572 190 | // \ 2023-09-12T10:46:50,572 | ^ 2023-09-12T10:46:50,573 ./src/builder.cpp:197:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:46:50,574 197 | // \ \ 2023-09-12T10:46:50,574 | ^ 2023-09-12T10:46:50,575 ./src/builder.cpp:199:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:46:50,575 199 | // \ 2023-09-12T10:46:50,576 | ^ 2023-09-12T10:46:50,576 ./src/builder.cpp:265:7: warning: multi-line comment [-Wcomment] 2023-09-12T10:46:50,576 265 | // \ \ 2023-09-12T10:46:50,577 | ^ 2023-09-12T10:46:50,579 ./src/builder.cpp:1215:5: warning: multi-line comment [-Wcomment] 2023-09-12T10:46:50,580 1215 | // / / v2 / \ 2023-09-12T10:46:50,580 | ^ 2023-09-12T10:46:50,582 ./src/builder.cpp:1324:9: warning: multi-line comment [-Wcomment] 2023-09-12T10:46:50,582 1324 | // / \ 2023-09-12T10:46:50,583 | ^ 2023-09-12T10:46:51,778 In file included from include/openbabel/builder.h:29, 2023-09-12T10:46:51,778 from ./src/builder.cpp:22: 2023-09-12T10:46:51,779 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:46:51,779 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:46:51,780 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:46:51,780 | ^ 2023-09-12T10:46:51,781 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:51,781 37 | # define UNUSED(x) x 2023-09-12T10:46:51,782 | ^ 2023-09-12T10:46:52,588 In file included from include/openbabel/mol.h:52, 2023-09-12T10:46:52,589 from include/openbabel/builder.h:30: 2023-09-12T10:46:52,589 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:52,590 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:52,590 862 | {return new OBVibrationData(*this);} 2023-09-12T10:46:52,591 | ^ 2023-09-12T10:46:52,592 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:46:52,593 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:46:52,594 | ^~~~~~~~ 2023-09-12T10:46:52,597 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:52,598 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:52,599 907 | {return new OBDOSData(*this);} 2023-09-12T10:46:52,599 | ^ 2023-09-12T10:46:52,600 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:46:52,600 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:46:52,601 | ^~~~~~~~ 2023-09-12T10:46:52,619 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:52,620 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:52,621 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:46:52,622 | ^ 2023-09-12T10:46:52,622 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:46:52,623 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:46:52,623 | ^~~~~~~~ 2023-09-12T10:46:52,628 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:46:52,629 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:46:52,630 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:46:52,630 | ^ 2023-09-12T10:46:52,631 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:46:52,631 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:46:52,632 | ^~~~~~~~ 2023-09-12T10:46:52,943 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:46:52,944 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:46:52,944 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:46:52,945 | ^ 2023-09-12T10:46:52,946 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:52,947 37 | # define UNUSED(x) x 2023-09-12T10:46:52,947 | ^ 2023-09-12T10:46:52,948 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:46:52,949 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:46:52,950 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:46:52,950 | ^ 2023-09-12T10:46:52,951 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:46:52,952 37 | # define UNUSED(x) x 2023-09-12T10:46:52,952 | ^ 2023-09-12T10:46:53,032 In file included from include/openbabel/format.h:22, 2023-09-12T10:46:53,033 from include/openbabel/obconversion.h:37, 2023-09-12T10:46:53,033 from ./src/builder.cpp:31: 2023-09-12T10:46:53,034 include/openbabel/plugin.h: At global scope: 2023-09-12T10:46:53,034 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:46:53,035 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:46:53,036 | ^~~~~~~~~~~~~~~ 2023-09-12T10:46:53,036 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:46:53,037 from /usr/include/c++/12/vector:66, 2023-09-12T10:46:53,038 from include/openbabel/builder.h:23: 2023-09-12T10:46:53,038 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:46:53,039 131 | struct binary_function 2023-09-12T10:46:53,040 | ^~~~~~~~~~~~~~~ 2023-09-12T10:47:01,509 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:47:01,510 /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]’: 2023-09-12T10:47:01,510 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:47:01,511 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:47:01,511 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:47:01,954 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:47:01,954 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:47:01,955 inlined from ‘void OpenBabel::OBBuilder::LoadFragments()’ at ./src/builder.cpp:109:25: 2023-09-12T10:47:01,955 /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 2023-09-12T10:47:01,956 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:47:01,956 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:47:04,347 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:47:04,348 inlined from ‘static void OpenBabel::OBBuilder::ConnectFrags(OpenBabel::OBMol&, OpenBabel::OBMol&, std::vector, std::vector, std::vector)’ at ./src/builder.cpp:1243:26: 2023-09-12T10:47:04,348 /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 2023-09-12T10:47:04,349 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:47:04,350 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:47:05,983 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:05,983 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/ccaWaNHx.s 2023-09-12T10:47:05,989 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:47:06,753 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/ 2023-09-12T10:47:06,754 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/ 2023-09-12T10:47:06,754 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:47:06,757 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 2023-09-12T10:47:06,762 Using built-in specs. 2023-09-12T10:47:06,763 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:47:06,763 Target: arm-linux-gnueabihf 2023-09-12T10:47:06,764 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 2023-09-12T10:47:06,764 Thread model: posix 2023-09-12T10:47:06,765 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:47:06,765 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:47:06,766 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:06,767 /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/ccpE3ARU.s 2023-09-12T10:47:06,776 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:06,777 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:06,778 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:06,779 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:06,779 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:47:06,780 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:47:06,781 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:47:06,781 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:47:06,782 ignoring duplicate directory "/usr/include/" 2023-09-12T10:47:06,783 as it is a non-system directory that duplicates a system directory 2023-09-12T10:47:06,784 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:47:06,784 #include "..." search starts here: 2023-09-12T10:47:06,785 #include <...> search starts here: 2023-09-12T10:47:06,785 /usr/include/eigen3 2023-09-12T10:47:06,786 include 2023-09-12T10:47:06,786 /usr/include/python3.11 2023-09-12T10:47:06,787 /usr/include/c++/12 2023-09-12T10:47:06,787 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:47:06,788 /usr/include/c++/12/backward 2023-09-12T10:47:06,788 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:47:06,788 /usr/local/include 2023-09-12T10:47:06,789 /usr/include/arm-linux-gnueabihf 2023-09-12T10:47:06,790 /usr/include 2023-09-12T10:47:06,790 End of search list. 2023-09-12T10:47:06,790 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:06,791 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:06,792 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:06,793 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:06,797 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:47:08,328 In file included from include/openbabel/stereo/stereo.h:27, 2023-09-12T10:47:08,329 from include/openbabel/graphsym.h:25, 2023-09-12T10:47:08,329 from ./src/canon.cpp:22: 2023-09-12T10:47:08,330 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:47:08,331 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:47:08,331 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:47:08,332 | ^ 2023-09-12T10:47:08,333 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:47:08,333 37 | # define UNUSED(x) x 2023-09-12T10:47:08,334 | ^ 2023-09-12T10:47:09,145 In file included from include/openbabel/mol.h:52, 2023-09-12T10:47:09,145 from include/openbabel/isomorphism.h:27, 2023-09-12T10:47:09,146 from include/openbabel/stereo/stereo.h:28: 2023-09-12T10:47:09,147 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:09,148 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:09,148 862 | {return new OBVibrationData(*this);} 2023-09-12T10:47:09,149 | ^ 2023-09-12T10:47:09,150 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:47:09,151 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:47:09,152 | ^~~~~~~~ 2023-09-12T10:47:09,152 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:09,153 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:09,154 907 | {return new OBDOSData(*this);} 2023-09-12T10:47:09,155 | ^ 2023-09-12T10:47:09,156 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:47:09,156 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:47:09,157 | ^~~~~~~~ 2023-09-12T10:47:09,171 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:09,171 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:09,172 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:47:09,172 | ^ 2023-09-12T10:47:09,173 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:47:09,174 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:47:09,174 | ^~~~~~~~ 2023-09-12T10:47:09,177 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:09,178 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:09,178 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:47:09,179 | ^ 2023-09-12T10:47:09,180 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:47:09,180 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:47:09,181 | ^~~~~~~~ 2023-09-12T10:47:09,629 ./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)’: 2023-09-12T10:47:09,630 ./src/canon.cpp:708:34: warning: ‘OpenBabel::CanonicalLabelsImpl::State::stereoCenters’ will be initialized after [-Wreorder] 2023-09-12T10:47:09,630 708 | std::vector &stereoCenters; 2023-09-12T10:47:09,631 | ^~~~~~~~~~~~~ 2023-09-12T10:47:09,632 ./src/canon.cpp:702:18: warning: ‘const bool OpenBabel::CanonicalLabelsImpl::State::onlyOne’ [-Wreorder] 2023-09-12T10:47:09,633 702 | const bool onlyOne; 2023-09-12T10:47:09,633 | ^~~~~~~ 2023-09-12T10:47:09,634 ./src/canon.cpp:683:7: warning: when initialized here [-Wreorder] 2023-09-12T10:47:09,635 683 | State(const std::vector &_symmetry_classes, 2023-09-12T10:47:09,635 | ^~~~~ 2023-09-12T10:47:09,734 ./src/canon.cpp: In static member function ‘static void OpenBabel::CanonicalLabelsImpl::UpdateMcr(OpenBabel::OBBitVec&, Orbits&, OpenBabel::OBMol*, const std::vector&)’: 2023-09-12T10:47:09,735 ./src/canon.cpp:1134:65: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T10:47:09,736 1134 | static void UpdateMcr(OBBitVec &mcr, Orbits &orbits, OBMol *mol, const std::vector &bestLabels) 2023-09-12T10:47:09,737 | ~~~~~~~^~~ 2023-09-12T10:47:27,665 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/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/' 2023-09-12T10:47:27,666 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/ccpE3ARU.s 2023-09-12T10:47:27,671 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:47:29,076 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/ 2023-09-12T10:47:29,077 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/ 2023-09-12T10:47:29,077 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:47:29,083 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 2023-09-12T10:47:29,088 Using built-in specs. 2023-09-12T10:47:29,088 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:47:29,089 Target: arm-linux-gnueabihf 2023-09-12T10:47:29,090 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 2023-09-12T10:47:29,090 Thread model: posix 2023-09-12T10:47:29,091 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:47:29,092 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:47:29,092 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:29,093 /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/ccI7EgAo.s 2023-09-12T10:47:29,101 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:29,102 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:29,103 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:29,103 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:29,103 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:47:29,104 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:47:29,104 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:47:29,105 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:47:29,105 ignoring duplicate directory "/usr/include/" 2023-09-12T10:47:29,106 as it is a non-system directory that duplicates a system directory 2023-09-12T10:47:29,106 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:47:29,107 #include "..." search starts here: 2023-09-12T10:47:29,108 #include <...> search starts here: 2023-09-12T10:47:29,108 /usr/include/eigen3 2023-09-12T10:47:29,109 include 2023-09-12T10:47:29,110 /usr/include/python3.11 2023-09-12T10:47:29,110 /usr/include/c++/12 2023-09-12T10:47:29,111 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:47:29,111 /usr/include/c++/12/backward 2023-09-12T10:47:29,112 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:47:29,112 /usr/local/include 2023-09-12T10:47:29,113 /usr/include/arm-linux-gnueabihf 2023-09-12T10:47:29,114 /usr/include 2023-09-12T10:47:29,114 End of search list. 2023-09-12T10:47:29,115 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:29,116 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:29,117 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:29,118 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:29,120 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:47:30,673 In file included from include/openbabel/atom.h:33, 2023-09-12T10:47:30,674 from include/openbabel/mol.h:43, 2023-09-12T10:47:30,674 from ./src/chains.cpp:33: 2023-09-12T10:47:30,675 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:47:30,676 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:47:30,676 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:47:30,677 | ^ 2023-09-12T10:47:30,678 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:47:30,678 37 | # define UNUSED(x) x 2023-09-12T10:47:30,679 | ^ 2023-09-12T10:47:31,434 In file included from include/openbabel/mol.h:52: 2023-09-12T10:47:31,435 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:31,435 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:31,436 862 | {return new OBVibrationData(*this);} 2023-09-12T10:47:31,436 | ^ 2023-09-12T10:47:31,437 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:47:31,438 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:47:31,438 | ^~~~~~~~ 2023-09-12T10:47:31,439 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:31,440 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:31,440 907 | {return new OBDOSData(*this);} 2023-09-12T10:47:31,441 | ^ 2023-09-12T10:47:31,441 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:47:31,442 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:47:31,443 | ^~~~~~~~ 2023-09-12T10:47:31,458 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:31,459 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:31,460 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:47:31,460 | ^ 2023-09-12T10:47:31,461 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:47:31,462 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:47:31,463 | ^~~~~~~~ 2023-09-12T10:47:31,465 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:31,466 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:31,466 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:47:31,467 | ^ 2023-09-12T10:47:31,467 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:47:31,468 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:47:31,469 | ^~~~~~~~ 2023-09-12T10:47:35,663 ./src/chains.cpp: In member function ‘void OpenBabel::OBChainsParser::ConstrainBackbone(OpenBabel::OBMol&, OpenBabel::Template*, int)’: 2023-09-12T10:47:35,663 ./src/chains.cpp:1271:51: warning: ‘nd’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:47:35,664 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:47:35,665 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:47:35,666 ./src/chains.cpp:1219:25: note: ‘nd’ was declared here 2023-09-12T10:47:35,666 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:47:35,667 | ^~ 2023-09-12T10:47:35,667 ./src/chains.cpp:1271:51: warning: ‘nc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:47:35,668 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:47:35,668 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:47:35,669 ./src/chains.cpp:1219:21: note: ‘nc’ was declared here 2023-09-12T10:47:35,669 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:47:35,670 | ^~ 2023-09-12T10:47:35,670 ./src/chains.cpp:1271:51: warning: ‘nb’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:47:35,671 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:47:35,671 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:47:35,672 ./src/chains.cpp:1219:17: note: ‘nb’ was declared here 2023-09-12T10:47:35,672 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:47:35,673 | ^~ 2023-09-12T10:47:35,673 ./src/chains.cpp:1271:51: warning: ‘na’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:47:35,674 1271 | result = Match4Constraints(pep,na,nb,nc,nd); 2023-09-12T10:47:35,674 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:47:35,675 ./src/chains.cpp:1219:13: note: ‘na’ was declared here 2023-09-12T10:47:35,675 1219 | OBAtom *na,*nb,*nc,*nd; 2023-09-12T10:47:35,676 | ^~ 2023-09-12T10:47:40,328 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:40,329 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/ccI7EgAo.s 2023-09-12T10:47:40,335 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:47:40,893 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/ 2023-09-12T10:47:40,894 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/ 2023-09-12T10:47:40,895 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:47:40,897 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 2023-09-12T10:47:40,901 Using built-in specs. 2023-09-12T10:47:40,902 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:47:40,903 Target: arm-linux-gnueabihf 2023-09-12T10:47:40,903 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 2023-09-12T10:47:40,904 Thread model: posix 2023-09-12T10:47:40,904 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:47:40,905 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:47:40,905 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/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/' 2023-09-12T10:47:40,906 /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/ccC3rSiC.s 2023-09-12T10:47:40,914 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:40,915 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 2023-09-12T10:47:40,916 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:40,917 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:40,917 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:47:40,918 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:47:40,918 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:47:40,919 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:47:40,920 ignoring duplicate directory "/usr/include/" 2023-09-12T10:47:40,920 as it is a non-system directory that duplicates a system directory 2023-09-12T10:47:40,921 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:47:40,921 #include "..." search starts here: 2023-09-12T10:47:40,922 #include <...> search starts here: 2023-09-12T10:47:40,923 /usr/include/eigen3 2023-09-12T10:47:40,923 include 2023-09-12T10:47:40,924 /usr/include/python3.11 2023-09-12T10:47:40,924 /usr/include/c++/12 2023-09-12T10:47:40,924 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:47:40,925 /usr/include/c++/12/backward 2023-09-12T10:47:40,925 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:47:40,926 /usr/local/include 2023-09-12T10:47:40,926 /usr/include/arm-linux-gnueabihf 2023-09-12T10:47:40,926 /usr/include 2023-09-12T10:47:40,927 End of search list. 2023-09-12T10:47:40,927 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:40,928 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:40,929 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:40,929 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:40,932 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:47:42,274 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:47:42,275 from ./src/chargemodel.cpp:21: 2023-09-12T10:47:42,275 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:47:42,276 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:47:42,276 | ^~~~~~~~~~~~~~~ 2023-09-12T10:47:42,277 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:47:42,278 from include/openbabel/plugin.h:23: 2023-09-12T10:47:42,278 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:47:42,279 131 | struct binary_function 2023-09-12T10:47:42,280 | ^~~~~~~~~~~~~~~ 2023-09-12T10:47:42,422 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:47:42,423 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:47:42,423 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:47:42,424 | ~~~~~~~^ 2023-09-12T10:47:42,425 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:47:42,426 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:47:42,426 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:47:42,427 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:47:42,540 In file included from include/openbabel/atom.h:33, 2023-09-12T10:47:42,541 from include/openbabel/mol.h:43, 2023-09-12T10:47:42,541 from ./src/chargemodel.cpp:22: 2023-09-12T10:47:42,542 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:47:42,543 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:47:42,543 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:47:42,544 | ^ 2023-09-12T10:47:42,545 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:47:42,546 37 | # define UNUSED(x) x 2023-09-12T10:47:42,546 | ^ 2023-09-12T10:47:43,276 In file included from include/openbabel/mol.h:52: 2023-09-12T10:47:43,277 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:43,278 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:43,278 862 | {return new OBVibrationData(*this);} 2023-09-12T10:47:43,279 | ^ 2023-09-12T10:47:43,280 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:47:43,280 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:47:43,281 | ^~~~~~~~ 2023-09-12T10:47:43,281 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:43,282 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:43,283 907 | {return new OBDOSData(*this);} 2023-09-12T10:47:43,283 | ^ 2023-09-12T10:47:43,284 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:47:43,284 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:47:43,285 | ^~~~~~~~ 2023-09-12T10:47:43,300 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:43,301 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:43,302 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:47:43,302 | ^ 2023-09-12T10:47:43,303 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:47:43,304 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:47:43,305 | ^~~~~~~~ 2023-09-12T10:47:43,307 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:43,308 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:43,308 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:47:43,309 | ^ 2023-09-12T10:47:43,310 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:47:43,311 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:47:43,311 | ^~~~~~~~ 2023-09-12T10:47:44,925 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:47:44,926 from include/openbabel/plugin.h:25: 2023-09-12T10:47:44,927 /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]’: 2023-09-12T10:47:44,927 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:47:44,928 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:47:44,929 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:47:44,970 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:47:44,971 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, 2023-09-12T10:47:44,971 inlined from ‘void OpenBabel::OBChargeModel::FillChargeVectors(OpenBabel::OBMol&)’ at ./src/chargemodel.cpp:44:35: 2023-09-12T10:47:44,972 /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 2023-09-12T10:47:44,972 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:47:44,973 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:47:44,974 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:47:44,974 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, 2023-09-12T10:47:44,975 inlined from ‘void OpenBabel::OBChargeModel::FillChargeVectors(OpenBabel::OBMol&)’ at ./src/chargemodel.cpp:45:34: 2023-09-12T10:47:44,975 /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 2023-09-12T10:47:44,976 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:47:44,977 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:47:45,051 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:45,052 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/ccC3rSiC.s 2023-09-12T10:47:45,056 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:47:45,106 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/ 2023-09-12T10:47:45,107 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/ 2023-09-12T10:47:45,107 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:47:45,108 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 2023-09-12T10:47:45,112 Using built-in specs. 2023-09-12T10:47:45,113 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:47:45,114 Target: arm-linux-gnueabihf 2023-09-12T10:47:45,114 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 2023-09-12T10:47:45,115 Thread model: posix 2023-09-12T10:47:45,115 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:47:45,116 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:47:45,116 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:45,117 /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/cczgIiFN.s 2023-09-12T10:47:45,125 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:45,126 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:45,127 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:45,128 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:45,128 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:47:45,129 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:47:45,129 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:47:45,130 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:47:45,131 ignoring duplicate directory "/usr/include/" 2023-09-12T10:47:45,132 as it is a non-system directory that duplicates a system directory 2023-09-12T10:47:45,132 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:47:45,132 #include "..." search starts here: 2023-09-12T10:47:45,133 #include <...> search starts here: 2023-09-12T10:47:45,133 /usr/include/eigen3 2023-09-12T10:47:45,134 include 2023-09-12T10:47:45,134 /usr/include/python3.11 2023-09-12T10:47:45,134 /usr/include/c++/12 2023-09-12T10:47:45,135 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:47:45,135 /usr/include/c++/12/backward 2023-09-12T10:47:45,136 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:47:45,136 /usr/local/include 2023-09-12T10:47:45,137 /usr/include/arm-linux-gnueabihf 2023-09-12T10:47:45,137 /usr/include 2023-09-12T10:47:45,137 End of search list. 2023-09-12T10:47:45,138 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:45,138 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 2023-09-12T10:47:45,139 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:45,140 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:45,143 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:47:46,496 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:47:46,496 from ./src/charges/eem.cpp:23: 2023-09-12T10:47:46,497 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:47:46,498 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:47:46,499 | ^~~~~~~~~~~~~~~ 2023-09-12T10:47:46,501 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:47:46,502 from ./src/charges/eem.cpp:19: 2023-09-12T10:47:46,503 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:47:46,504 131 | struct binary_function 2023-09-12T10:47:46,505 | ^~~~~~~~~~~~~~~ 2023-09-12T10:47:46,644 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:47:46,644 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:47:46,645 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:47:46,646 | ~~~~~~~^ 2023-09-12T10:47:46,647 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:47:46,647 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:47:46,648 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:47:46,649 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:47:46,762 In file included from include/openbabel/atom.h:33, 2023-09-12T10:47:46,763 from include/openbabel/mol.h:43, 2023-09-12T10:47:46,764 from ./src/charges/eem.cpp:24: 2023-09-12T10:47:46,764 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:47:46,765 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:47:46,766 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:47:46,767 | ^ 2023-09-12T10:47:46,767 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:47:46,768 37 | # define UNUSED(x) x 2023-09-12T10:47:46,769 | ^ 2023-09-12T10:47:47,498 In file included from include/openbabel/mol.h:52: 2023-09-12T10:47:47,498 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:47,499 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:47,500 862 | {return new OBVibrationData(*this);} 2023-09-12T10:47:47,500 | ^ 2023-09-12T10:47:47,501 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:47:47,501 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:47:47,502 | ^~~~~~~~ 2023-09-12T10:47:47,503 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:47,504 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:47,504 907 | {return new OBDOSData(*this);} 2023-09-12T10:47:47,505 | ^ 2023-09-12T10:47:47,505 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:47:47,506 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:47:47,507 | ^~~~~~~~ 2023-09-12T10:47:47,522 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:47,523 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:47,524 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:47:47,524 | ^ 2023-09-12T10:47:47,525 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:47:47,526 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:47:47,527 | ^~~~~~~~ 2023-09-12T10:47:47,528 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:47,529 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:47,530 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:47:47,530 | ^ 2023-09-12T10:47:47,531 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:47:47,532 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:47:47,533 | ^~~~~~~~ 2023-09-12T10:47:50,457 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:47:50,596 from ./src/charges/eem.cpp:20: 2023-09-12T10:47:50,597 /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]’: 2023-09-12T10:47:50,598 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:47:50,600 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:47:50,601 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:47:50,618 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:47:50,618 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::EEMParameter; _Alloc = std::allocator]’, 2023-09-12T10:47:50,619 inlined from ‘void OpenBabel::EEMCharges::_loadParameters()’ at ./src/charges/eem.cpp:109:28: 2023-09-12T10:47:50,620 /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 2023-09-12T10:47:50,620 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:47:50,622 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:47:51,951 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:51,952 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/cczgIiFN.s 2023-09-12T10:47:51,956 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:47:52,230 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/ 2023-09-12T10:47:52,231 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/ 2023-09-12T10:47:52,231 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/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.' 2023-09-12T10:47:52,233 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 2023-09-12T10:47:52,237 Using built-in specs. 2023-09-12T10:47:52,238 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:47:52,238 Target: arm-linux-gnueabihf 2023-09-12T10:47:52,239 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 2023-09-12T10:47:52,240 Thread model: posix 2023-09-12T10:47:52,240 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:47:52,241 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:47:52,241 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:47:52,242 /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/cccHQyli.s 2023-09-12T10:47:52,250 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:52,251 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:52,252 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:52,253 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:52,253 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:47:52,254 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:47:52,254 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:47:52,255 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:47:52,255 ignoring duplicate directory "/usr/include/" 2023-09-12T10:47:52,256 as it is a non-system directory that duplicates a system directory 2023-09-12T10:47:52,257 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:47:52,257 #include "..." search starts here: 2023-09-12T10:47:52,258 #include <...> search starts here: 2023-09-12T10:47:52,258 /usr/include/eigen3 2023-09-12T10:47:52,259 include 2023-09-12T10:47:52,260 /usr/include/python3.11 2023-09-12T10:47:52,260 /usr/include/c++/12 2023-09-12T10:47:52,261 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:47:52,261 /usr/include/c++/12/backward 2023-09-12T10:47:52,262 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:47:52,263 /usr/local/include 2023-09-12T10:47:52,263 /usr/include/arm-linux-gnueabihf 2023-09-12T10:47:52,264 /usr/include 2023-09-12T10:47:52,264 End of search list. 2023-09-12T10:47:52,265 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:47:52,265 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:47:52,266 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:47:52,266 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:47:52,272 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:47:53,873 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:47:53,874 from include/charges/eqeq.h:22, 2023-09-12T10:47:53,874 from ./src/charges/eqeq.cpp:19: 2023-09-12T10:47:53,875 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:47:53,876 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:47:53,876 | ^~~~~~~~~~~~~~~ 2023-09-12T10:47:53,877 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:47:53,877 from include/openbabel/plugin.h:23: 2023-09-12T10:47:53,878 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:47:53,879 131 | struct binary_function 2023-09-12T10:47:53,880 | ^~~~~~~~~~~~~~~ 2023-09-12T10:47:54,019 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:47:54,019 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:47:54,020 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:47:54,021 | ~~~~~~~^ 2023-09-12T10:47:54,022 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:47:54,022 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:47:54,023 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:47:54,024 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:47:54,137 In file included from include/openbabel/atom.h:33, 2023-09-12T10:47:54,138 from include/openbabel/mol.h:43, 2023-09-12T10:47:54,138 from include/charges/eqeq.h:23: 2023-09-12T10:47:54,139 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:47:54,140 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:47:54,140 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:47:54,141 | ^ 2023-09-12T10:47:54,142 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:47:54,142 37 | # define UNUSED(x) x 2023-09-12T10:47:54,143 | ^ 2023-09-12T10:47:54,875 In file included from include/openbabel/mol.h:52: 2023-09-12T10:47:54,876 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:54,877 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:54,878 862 | {return new OBVibrationData(*this);} 2023-09-12T10:47:54,879 | ^ 2023-09-12T10:47:54,879 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:47:54,880 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:47:54,880 | ^~~~~~~~ 2023-09-12T10:47:54,882 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:54,882 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:54,883 907 | {return new OBDOSData(*this);} 2023-09-12T10:47:54,883 | ^ 2023-09-12T10:47:54,884 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:47:54,884 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:47:54,885 | ^~~~~~~~ 2023-09-12T10:47:54,901 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:54,902 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:54,903 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:47:54,904 | ^ 2023-09-12T10:47:54,904 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:47:54,905 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:47:54,906 | ^~~~~~~~ 2023-09-12T10:47:54,909 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:47:54,910 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:47:54,910 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:47:54,911 | ^ 2023-09-12T10:47:54,912 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:47:54,913 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:47:54,913 | ^~~~~~~~ 2023-09-12T10:48:17,880 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:48:17,881 from include/openbabel/plugin.h:25: 2023-09-12T10:48:17,882 /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]’: 2023-09-12T10:48:17,882 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:48:17,883 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:48:17,884 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:20,175 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:48:20,175 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, 2023-09-12T10:48:20,176 inlined from ‘virtual bool OpenBabel::EQEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/eqeq.cpp:187:33: 2023-09-12T10:48:20,176 /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 2023-09-12T10:48:20,177 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:48:20,177 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:20,178 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:48:20,179 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, 2023-09-12T10:48:20,179 inlined from ‘virtual bool OpenBabel::EQEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/eqeq.cpp:188:32: 2023-09-12T10:48:20,180 /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 2023-09-12T10:48:20,180 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:48:20,181 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:22,364 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/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/' 2023-09-12T10:48:22,365 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/charges/eqeq.o /tmp/cccHQyli.s 2023-09-12T10:48:22,370 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:24,381 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/ 2023-09-12T10:48:24,381 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/ 2023-09-12T10:48:24,382 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/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.' 2023-09-12T10:48:24,393 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 2023-09-12T10:48:24,398 Using built-in specs. 2023-09-12T10:48:24,399 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:24,400 Target: arm-linux-gnueabihf 2023-09-12T10:48:24,400 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 2023-09-12T10:48:24,401 Thread model: posix 2023-09-12T10:48:24,401 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:24,401 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:24,402 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/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/' 2023-09-12T10:48:24,402 /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/cclfE2Kz.s 2023-09-12T10:48:24,411 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:24,412 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 2023-09-12T10:48:24,413 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:24,414 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:24,414 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:24,415 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:24,415 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:24,416 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:24,417 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:24,417 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:24,418 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:24,419 #include "..." search starts here: 2023-09-12T10:48:24,419 #include <...> search starts here: 2023-09-12T10:48:24,420 /usr/include/eigen3 2023-09-12T10:48:24,420 include 2023-09-12T10:48:24,421 /usr/include/python3.11 2023-09-12T10:48:24,421 /usr/include/c++/12 2023-09-12T10:48:24,422 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:24,422 /usr/include/c++/12/backward 2023-09-12T10:48:24,423 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:24,423 /usr/local/include 2023-09-12T10:48:24,423 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:24,424 /usr/include 2023-09-12T10:48:24,424 End of search list. 2023-09-12T10:48:24,425 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:24,425 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:24,426 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:24,426 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:24,432 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:25,797 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:48:25,797 from ./src/charges/fromfile.cpp:21: 2023-09-12T10:48:25,798 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:48:25,798 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:48:25,799 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:25,800 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:48:25,800 from include/openbabel/plugin.h:23: 2023-09-12T10:48:25,801 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:48:25,801 131 | struct binary_function 2023-09-12T10:48:25,802 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:25,946 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:48:25,947 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:48:25,948 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:48:25,948 | ~~~~~~~^ 2023-09-12T10:48:25,949 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:48:25,950 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:48:25,951 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:48:25,951 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:48:26,065 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:26,066 from include/openbabel/mol.h:43, 2023-09-12T10:48:26,067 from ./src/charges/fromfile.cpp:22: 2023-09-12T10:48:26,067 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:26,068 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:26,069 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:26,069 | ^ 2023-09-12T10:48:26,070 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:26,071 37 | # define UNUSED(x) x 2023-09-12T10:48:26,072 | ^ 2023-09-12T10:48:26,803 In file included from include/openbabel/mol.h:52: 2023-09-12T10:48:26,803 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:26,804 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:26,805 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:26,805 | ^ 2023-09-12T10:48:26,806 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:26,806 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:26,807 | ^~~~~~~~ 2023-09-12T10:48:26,809 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:26,810 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:26,810 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:26,811 | ^ 2023-09-12T10:48:26,811 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:26,812 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:26,812 | ^~~~~~~~ 2023-09-12T10:48:26,829 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:26,830 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:26,830 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:26,831 | ^ 2023-09-12T10:48:26,832 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:26,833 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:26,834 | ^~~~~~~~ 2023-09-12T10:48:26,836 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:26,837 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:26,838 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:26,839 | ^ 2023-09-12T10:48:26,839 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:26,840 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:26,841 | ^~~~~~~~ 2023-09-12T10:48:27,262 ./src/charges/fromfile.cpp: In member function ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:48:27,263 ./src/charges/fromfile.cpp:96:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:48:27,264 96 | for ( int i = 1; i <= mol.NumAtoms(); i++) 2023-09-12T10:48:27,265 | ~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,100 In file included from /usr/include/c++/12/map:60, 2023-09-12T10:48:30,100 from include/openbabel/plugin.h:26: 2023-09-12T10:48:30,101 /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> >]’: 2023-09-12T10:48:30,101 /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 2023-09-12T10:48:30,102 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T10:48:30,103 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,720 In file included from /usr/include/c++/12/map:61: 2023-09-12T10:48:30,720 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> >]’, 2023-09-12T10:48:30,721 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:112:32: 2023-09-12T10:48:30,722 /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 2023-09-12T10:48:30,723 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:48:30,724 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,724 531 | std::forward_as_tuple(std::move(__k)), 2023-09-12T10:48:30,725 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,726 532 | std::tuple<>()); 2023-09-12T10:48:30,726 | ~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,727 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> >]’, 2023-09-12T10:48:30,728 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:120:32: 2023-09-12T10:48:30,728 /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 2023-09-12T10:48:30,729 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:48:30,730 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,731 531 | std::forward_as_tuple(std::move(__k)), 2023-09-12T10:48:30,731 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,732 532 | std::tuple<>()); 2023-09-12T10:48:30,732 | ~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,733 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> >]’, 2023-09-12T10:48:30,733 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:128:32: 2023-09-12T10:48:30,734 /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 2023-09-12T10:48:30,735 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:48:30,735 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,736 531 | std::forward_as_tuple(std::move(__k)), 2023-09-12T10:48:30,737 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:30,738 532 | std::tuple<>()); 2023-09-12T10:48:30,739 | ~~~~~~~~~~~~~~~ 2023-09-12T10:48:31,563 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:48:31,564 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/cclfE2Kz.s 2023-09-12T10:48:31,569 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:31,872 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/ 2023-09-12T10:48:31,873 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/ 2023-09-12T10:48:31,874 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:48:31,875 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 2023-09-12T10:48:31,879 Using built-in specs. 2023-09-12T10:48:31,880 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:31,880 Target: arm-linux-gnueabihf 2023-09-12T10:48:31,881 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 2023-09-12T10:48:31,881 Thread model: posix 2023-09-12T10:48:31,882 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:31,882 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:31,883 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:48:31,884 /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/ccrU2rY4.s 2023-09-12T10:48:31,892 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:31,893 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:31,894 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:31,895 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:31,896 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:31,897 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:31,897 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:31,898 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:31,898 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:31,898 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:31,899 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:31,899 #include "..." search starts here: 2023-09-12T10:48:31,900 #include <...> search starts here: 2023-09-12T10:48:31,900 /usr/include/eigen3 2023-09-12T10:48:31,901 include 2023-09-12T10:48:31,901 /usr/include/python3.11 2023-09-12T10:48:31,902 /usr/include/c++/12 2023-09-12T10:48:31,902 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:31,902 /usr/include/c++/12/backward 2023-09-12T10:48:31,903 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:31,903 /usr/local/include 2023-09-12T10:48:31,904 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:31,904 /usr/include 2023-09-12T10:48:31,905 End of search list. 2023-09-12T10:48:31,905 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:31,906 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:31,907 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:31,907 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:31,912 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:33,269 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:48:33,269 from ./src/charges/gasteiger.cpp:20: 2023-09-12T10:48:33,270 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:48:33,271 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:48:33,272 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:33,273 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:48:33,273 from include/openbabel/plugin.h:23: 2023-09-12T10:48:33,274 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:48:33,275 131 | struct binary_function 2023-09-12T10:48:33,276 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:33,421 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:48:33,422 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:48:33,422 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:48:33,423 | ~~~~~~~^ 2023-09-12T10:48:33,424 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:48:33,424 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:48:33,425 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:48:33,426 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:48:33,545 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:33,546 from include/openbabel/mol.h:43, 2023-09-12T10:48:33,547 from ./src/charges/gasteiger.cpp:21: 2023-09-12T10:48:33,547 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:33,548 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:33,549 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:33,549 | ^ 2023-09-12T10:48:33,550 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:33,551 37 | # define UNUSED(x) x 2023-09-12T10:48:33,551 | ^ 2023-09-12T10:48:34,277 In file included from include/openbabel/mol.h:52: 2023-09-12T10:48:34,278 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:34,278 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:34,279 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:34,280 | ^ 2023-09-12T10:48:34,280 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:34,281 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:34,281 | ^~~~~~~~ 2023-09-12T10:48:34,283 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:34,284 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:34,284 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:34,285 | ^ 2023-09-12T10:48:34,286 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:34,287 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:34,287 | ^~~~~~~~ 2023-09-12T10:48:34,302 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:34,303 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:34,304 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:34,305 | ^ 2023-09-12T10:48:34,305 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:34,306 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:34,307 | ^~~~~~~~ 2023-09-12T10:48:34,309 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:34,310 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:34,311 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:34,312 | ^ 2023-09-12T10:48:34,312 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:34,313 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:34,315 | ^~~~~~~~ 2023-09-12T10:48:36,559 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/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/' 2023-09-12T10:48:36,560 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/charges/gasteiger.o /tmp/ccrU2rY4.s 2023-09-12T10:48:36,564 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:36,667 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/ 2023-09-12T10:48:36,668 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/ 2023-09-12T10:48:36,668 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/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.' 2023-09-12T10:48:36,669 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 2023-09-12T10:48:36,673 Using built-in specs. 2023-09-12T10:48:36,674 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:36,674 Target: arm-linux-gnueabihf 2023-09-12T10:48:36,675 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 2023-09-12T10:48:36,675 Thread model: posix 2023-09-12T10:48:36,676 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:36,676 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:36,677 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/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/' 2023-09-12T10:48:36,677 /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/cchb0hYj.s 2023-09-12T10:48:36,686 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:36,686 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:36,687 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:36,688 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:36,689 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:36,689 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:36,690 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:36,691 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:36,691 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:36,692 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:36,693 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:36,693 #include "..." search starts here: 2023-09-12T10:48:36,694 #include <...> search starts here: 2023-09-12T10:48:36,695 /usr/include/eigen3 2023-09-12T10:48:36,695 include 2023-09-12T10:48:36,696 /usr/include/python3.11 2023-09-12T10:48:36,697 /usr/include/c++/12 2023-09-12T10:48:36,697 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:36,698 /usr/include/c++/12/backward 2023-09-12T10:48:36,698 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:36,699 /usr/local/include 2023-09-12T10:48:36,700 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:36,701 /usr/include 2023-09-12T10:48:36,701 End of search list. 2023-09-12T10:48:36,702 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:36,702 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:36,703 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:36,704 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:36,706 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:38,088 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:48:38,089 from ./src/charges/mmff94.cpp:20: 2023-09-12T10:48:38,090 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:48:38,091 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:48:38,092 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:38,092 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:48:38,093 from include/openbabel/plugin.h:23: 2023-09-12T10:48:38,093 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:48:38,094 131 | struct binary_function 2023-09-12T10:48:38,094 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:38,241 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:48:38,242 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:48:38,243 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:48:38,243 | ~~~~~~~^ 2023-09-12T10:48:38,244 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:48:38,244 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:48:38,245 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:48:38,245 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:48:38,362 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:38,363 from include/openbabel/mol.h:43, 2023-09-12T10:48:38,364 from ./src/charges/mmff94.cpp:21: 2023-09-12T10:48:38,364 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:38,365 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:38,366 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:38,367 | ^ 2023-09-12T10:48:38,367 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:38,368 37 | # define UNUSED(x) x 2023-09-12T10:48:38,369 | ^ 2023-09-12T10:48:39,097 In file included from include/openbabel/mol.h:52: 2023-09-12T10:48:39,098 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:39,099 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:39,100 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:39,100 | ^ 2023-09-12T10:48:39,101 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:39,102 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:39,102 | ^~~~~~~~ 2023-09-12T10:48:39,103 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:39,104 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:39,105 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:39,105 | ^ 2023-09-12T10:48:39,106 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:39,107 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:39,108 | ^~~~~~~~ 2023-09-12T10:48:39,123 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:39,124 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:39,124 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:39,125 | ^ 2023-09-12T10:48:39,125 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:39,126 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:39,126 | ^~~~~~~~ 2023-09-12T10:48:39,130 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:39,130 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:39,131 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:39,131 | ^ 2023-09-12T10:48:39,132 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:39,133 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:39,134 | ^~~~~~~~ 2023-09-12T10:48:39,410 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:48:39,411 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,411 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,412 | ^ 2023-09-12T10:48:39,413 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,413 37 | # define UNUSED(x) x 2023-09-12T10:48:39,414 | ^ 2023-09-12T10:48:39,415 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:48:39,415 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,416 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,417 | ^ 2023-09-12T10:48:39,417 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,418 37 | # define UNUSED(x) x 2023-09-12T10:48:39,418 | ^ 2023-09-12T10:48:39,419 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:48:39,420 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,421 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,421 | ^ 2023-09-12T10:48:39,422 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,423 37 | # define UNUSED(x) x 2023-09-12T10:48:39,424 | ^ 2023-09-12T10:48:39,425 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:48:39,425 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,426 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,426 | ^ 2023-09-12T10:48:39,427 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,427 37 | # define UNUSED(x) x 2023-09-12T10:48:39,428 | ^ 2023-09-12T10:48:39,429 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:48:39,429 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,430 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,430 | ^ 2023-09-12T10:48:39,431 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,432 37 | # define UNUSED(x) x 2023-09-12T10:48:39,432 | ^ 2023-09-12T10:48:39,433 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:48:39,433 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,434 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,435 | ^ 2023-09-12T10:48:39,436 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,436 37 | # define UNUSED(x) x 2023-09-12T10:48:39,437 | ^ 2023-09-12T10:48:39,438 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:48:39,439 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,440 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,440 | ^ 2023-09-12T10:48:39,441 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,442 37 | # define UNUSED(x) x 2023-09-12T10:48:39,443 | ^ 2023-09-12T10:48:39,444 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:48:39,444 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:48:39,445 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:48:39,446 | ^ 2023-09-12T10:48:39,446 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:39,447 37 | # define UNUSED(x) x 2023-09-12T10:48:39,448 | ^ 2023-09-12T10:48:41,742 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:48:41,743 from include/openbabel/plugin.h:25: 2023-09-12T10:48:41,744 /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]’: 2023-09-12T10:48:41,745 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:48:41,745 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:48:41,746 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:41,812 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:48:41,813 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, 2023-09-12T10:48:41,814 inlined from ‘virtual bool OpenBabel::MMFF94Charges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/mmff94.cpp:68:33: 2023-09-12T10:48:41,814 /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 2023-09-12T10:48:41,815 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:48:41,815 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:41,816 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:48:41,816 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, 2023-09-12T10:48:41,817 inlined from ‘virtual bool OpenBabel::MMFF94Charges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/mmff94.cpp:69:32: 2023-09-12T10:48:41,818 /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 2023-09-12T10:48:41,818 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:48:41,819 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:48:42,019 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:48:42,020 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/cchb0hYj.s 2023-09-12T10:48:42,027 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:42,189 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/ 2023-09-12T10:48:42,189 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/ 2023-09-12T10:48:42,190 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/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.' 2023-09-12T10:48:42,191 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 2023-09-12T10:48:42,195 Using built-in specs. 2023-09-12T10:48:42,196 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:42,196 Target: arm-linux-gnueabihf 2023-09-12T10:48:42,197 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 2023-09-12T10:48:42,197 Thread model: posix 2023-09-12T10:48:42,198 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:42,199 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:42,199 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:48:42,200 /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/ccmaTNss.s 2023-09-12T10:48:42,210 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:42,210 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:42,212 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:42,212 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:42,213 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:42,213 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:42,214 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:42,214 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:42,215 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:42,216 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:42,216 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:42,217 #include "..." search starts here: 2023-09-12T10:48:42,218 #include <...> search starts here: 2023-09-12T10:48:42,218 /usr/include/eigen3 2023-09-12T10:48:42,218 include 2023-09-12T10:48:42,219 /usr/include/python3.11 2023-09-12T10:48:42,219 /usr/include/c++/12 2023-09-12T10:48:42,220 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:42,220 /usr/include/c++/12/backward 2023-09-12T10:48:42,221 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:42,221 /usr/local/include 2023-09-12T10:48:42,221 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:42,222 /usr/include 2023-09-12T10:48:42,222 End of search list. 2023-09-12T10:48:42,223 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:42,223 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:42,224 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:42,225 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:42,229 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:43,580 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:48:43,581 from ./src/charges/none.cpp:21: 2023-09-12T10:48:43,582 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:48:43,582 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:48:43,583 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:43,584 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:48:43,584 from include/openbabel/plugin.h:23: 2023-09-12T10:48:43,585 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:48:43,586 131 | struct binary_function 2023-09-12T10:48:43,586 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:43,729 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:48:43,729 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:48:43,730 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:48:43,731 | ~~~~~~~^ 2023-09-12T10:48:43,732 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:48:43,732 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:48:43,733 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:48:43,734 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:48:43,847 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:43,848 from include/openbabel/mol.h:43, 2023-09-12T10:48:43,849 from ./src/charges/none.cpp:22: 2023-09-12T10:48:43,849 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:43,850 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:43,851 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:43,851 | ^ 2023-09-12T10:48:43,852 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:43,853 37 | # define UNUSED(x) x 2023-09-12T10:48:43,853 | ^ 2023-09-12T10:48:44,592 In file included from include/openbabel/mol.h:52: 2023-09-12T10:48:44,593 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:44,594 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:44,594 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:44,595 | ^ 2023-09-12T10:48:44,595 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:44,596 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:44,596 | ^~~~~~~~ 2023-09-12T10:48:44,598 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:44,598 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:44,599 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:44,599 | ^ 2023-09-12T10:48:44,600 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:44,601 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:44,601 | ^~~~~~~~ 2023-09-12T10:48:44,617 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:44,618 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:44,619 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:44,619 | ^ 2023-09-12T10:48:44,620 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:44,621 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:44,622 | ^~~~~~~~ 2023-09-12T10:48:44,624 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:44,625 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:44,626 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:44,626 | ^ 2023-09-12T10:48:44,627 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:44,628 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:44,628 | ^~~~~~~~ 2023-09-12T10:48:46,868 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:48:46,869 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/ccmaTNss.s 2023-09-12T10:48:46,873 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:48:46,978 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/ 2023-09-12T10:48:46,979 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/ 2023-09-12T10:48:46,979 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:48:46,981 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/charges/qeq.cpp -o build/temp.linux-armv7l-cpython-311/./src/charges/qeq.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:48:46,984 Using built-in specs. 2023-09-12T10:48:46,985 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:48:46,986 Target: arm-linux-gnueabihf 2023-09-12T10:48:46,986 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 2023-09-12T10:48:46,987 Thread model: posix 2023-09-12T10:48:46,987 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:48:46,988 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:48:46,988 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:48:46,989 /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/cc83G8hi.s 2023-09-12T10:48:46,998 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:46,998 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:48:46,999 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:47,000 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:47,000 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:48:47,000 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:48:47,001 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:48:47,001 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:48:47,002 ignoring duplicate directory "/usr/include/" 2023-09-12T10:48:47,002 as it is a non-system directory that duplicates a system directory 2023-09-12T10:48:47,003 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:48:47,003 #include "..." search starts here: 2023-09-12T10:48:47,004 #include <...> search starts here: 2023-09-12T10:48:47,005 /usr/include/eigen3 2023-09-12T10:48:47,005 include 2023-09-12T10:48:47,006 /usr/include/python3.11 2023-09-12T10:48:47,006 /usr/include/c++/12 2023-09-12T10:48:47,007 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:48:47,008 /usr/include/c++/12/backward 2023-09-12T10:48:47,008 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:48:47,009 /usr/local/include 2023-09-12T10:48:47,009 /usr/include/arm-linux-gnueabihf 2023-09-12T10:48:47,010 /usr/include 2023-09-12T10:48:47,011 End of search list. 2023-09-12T10:48:47,011 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:48:47,012 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 2023-09-12T10:48:47,013 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:48:47,014 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:48:47,015 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:48:48,601 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:48:48,602 from include/charges/qeq.h:22, 2023-09-12T10:48:48,602 from ./src/charges/qeq.cpp:19: 2023-09-12T10:48:48,603 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:48:48,604 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:48:48,604 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:48,605 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:48:48,606 from include/openbabel/plugin.h:23: 2023-09-12T10:48:48,606 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:48:48,607 131 | struct binary_function 2023-09-12T10:48:48,608 | ^~~~~~~~~~~~~~~ 2023-09-12T10:48:48,747 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:48:48,748 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:48:48,748 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:48:48,749 | ~~~~~~~^ 2023-09-12T10:48:48,749 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:48:48,750 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:48:48,751 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:48:48,751 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:48:48,865 In file included from include/openbabel/atom.h:33, 2023-09-12T10:48:48,866 from include/openbabel/mol.h:43, 2023-09-12T10:48:48,866 from include/charges/qeq.h:23: 2023-09-12T10:48:48,867 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:48:48,867 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:48:48,868 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:48:48,868 | ^ 2023-09-12T10:48:48,869 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:48:48,870 37 | # define UNUSED(x) x 2023-09-12T10:48:48,870 | ^ 2023-09-12T10:48:49,604 In file included from include/openbabel/mol.h:52: 2023-09-12T10:48:49,604 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:49,605 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:49,606 862 | {return new OBVibrationData(*this);} 2023-09-12T10:48:49,607 | ^ 2023-09-12T10:48:49,607 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:48:49,608 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:48:49,609 | ^~~~~~~~ 2023-09-12T10:48:49,610 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:49,610 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:49,611 907 | {return new OBDOSData(*this);} 2023-09-12T10:48:49,612 | ^ 2023-09-12T10:48:49,612 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:48:49,613 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:48:49,614 | ^~~~~~~~ 2023-09-12T10:48:49,629 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:49,630 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:49,630 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:48:49,631 | ^ 2023-09-12T10:48:49,632 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:48:49,632 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:48:49,633 | ^~~~~~~~ 2023-09-12T10:48:49,635 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:48:49,636 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:48:49,636 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:48:49,637 | ^ 2023-09-12T10:48:49,637 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:48:49,638 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:48:49,639 | ^~~~~~~~ 2023-09-12T10:48:51,887 ./src/charges/qeq.cpp: In member function ‘Eigen::Vector3d OpenBabel::QEqCharges::GetParameters(unsigned int, int)’: 2023-09-12T10:48:51,888 ./src/charges/qeq.cpp:148:58: warning: unused parameter ‘Q’ [-Wunused-parameter] 2023-09-12T10:48:51,888 148 | Vector3d QEqCharges::GetParameters(unsigned int Z, int Q) 2023-09-12T10:48:51,889 | ~~~~^ 2023-09-12T10:49:25,519 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:49:25,520 from include/openbabel/plugin.h:25: 2023-09-12T10:49:25,520 /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 >]’: 2023-09-12T10:49:25,521 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:49:25,522 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:49:25,522 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:49:25,650 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:49:25,651 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Eigen::Matrix; _Alloc = std::allocator >]’, 2023-09-12T10:49:25,652 inlined from ‘void OpenBabel::QEqCharges::ParseParamFile()’ at ./src/charges/qeq.cpp:143:28: 2023-09-12T10:49:25,652 /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 2023-09-12T10:49:25,653 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:49:25,654 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:49:25,901 /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]’: 2023-09-12T10:49:25,902 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:49:25,903 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:49:25,903 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:49:26,054 /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]’: 2023-09-12T10:49:26,055 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:49:37,613 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:49:37,613 inlined from ‘virtual bool OpenBabel::QEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qeq.cpp:280:35: 2023-09-12T10:49:37,614 /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 2023-09-12T10:49:37,614 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:49:37,615 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:49:37,615 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:49:37,616 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, 2023-09-12T10:49:37,616 inlined from ‘virtual bool OpenBabel::QEqCharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qeq.cpp:281:34: 2023-09-12T10:49:37,617 /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 2023-09-12T10:49:37,618 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:49:37,618 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:49:41,956 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:49:41,957 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/cc83G8hi.s 2023-09-12T10:49:41,963 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:49:45,909 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/ 2023-09-12T10:49:45,910 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/ 2023-09-12T10:49:45,910 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:49:45,931 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 2023-09-12T10:49:45,938 Using built-in specs. 2023-09-12T10:49:45,939 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:49:45,939 Target: arm-linux-gnueabihf 2023-09-12T10:49:45,940 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 2023-09-12T10:49:45,940 Thread model: posix 2023-09-12T10:49:45,941 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:49:45,941 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:49:45,942 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/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/' 2023-09-12T10:49:45,942 /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/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/ccuAYJDs.s 2023-09-12T10:49:45,952 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:45,953 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 2023-09-12T10:49:45,954 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:45,955 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:45,955 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:49:45,956 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:49:45,956 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:49:45,957 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:49:45,957 ignoring duplicate directory "/usr/include/" 2023-09-12T10:49:45,958 as it is a non-system directory that duplicates a system directory 2023-09-12T10:49:45,958 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:49:45,959 #include "..." search starts here: 2023-09-12T10:49:45,960 #include <...> search starts here: 2023-09-12T10:49:45,960 /usr/include/eigen3 2023-09-12T10:49:45,961 include 2023-09-12T10:49:45,961 /usr/include/python3.11 2023-09-12T10:49:45,962 /usr/include/c++/12 2023-09-12T10:49:45,962 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:49:45,962 /usr/include/c++/12/backward 2023-09-12T10:49:45,963 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:49:45,963 /usr/local/include 2023-09-12T10:49:45,964 /usr/include/arm-linux-gnueabihf 2023-09-12T10:49:45,964 /usr/include 2023-09-12T10:49:45,965 End of search list. 2023-09-12T10:49:45,965 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:49:45,966 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:49:45,967 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:49:45,967 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:49:45,973 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:49:47,553 In file included from include/openbabel/chargemodel.h:24, 2023-09-12T10:49:47,554 from include/charges/qtpie.h:22, 2023-09-12T10:49:47,555 from ./src/charges/qtpie.cpp:19: 2023-09-12T10:49:47,555 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:49:47,556 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:49:47,556 | ^~~~~~~~~~~~~~~ 2023-09-12T10:49:47,557 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:49:47,558 from include/openbabel/plugin.h:23: 2023-09-12T10:49:47,559 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:49:47,559 131 | struct binary_function 2023-09-12T10:49:47,560 | ^~~~~~~~~~~~~~~ 2023-09-12T10:49:47,699 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2023-09-12T10:49:47,700 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2023-09-12T10:49:47,700 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2023-09-12T10:49:47,701 | ~~~~~~~^ 2023-09-12T10:49:47,702 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2023-09-12T10:49:47,702 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2023-09-12T10:49:47,703 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2023-09-12T10:49:47,704 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:49:47,817 In file included from include/openbabel/atom.h:33, 2023-09-12T10:49:47,818 from include/openbabel/mol.h:43, 2023-09-12T10:49:47,818 from include/charges/qtpie.h:23: 2023-09-12T10:49:47,819 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:49:47,820 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:49:47,820 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:49:47,821 | ^ 2023-09-12T10:49:47,822 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:49:47,823 37 | # define UNUSED(x) x 2023-09-12T10:49:47,824 | ^ 2023-09-12T10:49:48,557 In file included from include/openbabel/mol.h:52: 2023-09-12T10:49:48,557 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:48,558 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:48,559 862 | {return new OBVibrationData(*this);} 2023-09-12T10:49:48,559 | ^ 2023-09-12T10:49:48,560 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:49:48,560 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:49:48,561 | ^~~~~~~~ 2023-09-12T10:49:48,562 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:48,563 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:48,563 907 | {return new OBDOSData(*this);} 2023-09-12T10:49:48,564 | ^ 2023-09-12T10:49:48,564 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:49:48,565 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:49:48,566 | ^~~~~~~~ 2023-09-12T10:49:48,581 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:48,582 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:48,582 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:49:48,583 | ^ 2023-09-12T10:49:48,584 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:49:48,585 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:49:48,586 | ^~~~~~~~ 2023-09-12T10:49:48,587 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:49:48,588 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:49:48,589 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:49:48,590 | ^ 2023-09-12T10:49:48,590 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:49:48,591 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:49:48,592 | ^~~~~~~~ 2023-09-12T10:49:50,843 ./src/charges/qtpie.cpp: In member function ‘Eigen::Vector3d OpenBabel::QTPIECharges::GetParameters(unsigned int, int)’: 2023-09-12T10:49:50,844 ./src/charges/qtpie.cpp:145:60: warning: unused parameter ‘Q’ [-Wunused-parameter] 2023-09-12T10:49:50,845 145 | Vector3d QTPIECharges::GetParameters(unsigned int Z, int Q) 2023-09-12T10:49:50,846 | ~~~~^ 2023-09-12T10:50:24,497 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:50:24,497 from include/openbabel/plugin.h:25: 2023-09-12T10:50:24,498 /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 >]’: 2023-09-12T10:50:24,498 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:50:24,499 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:50:24,500 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:24,635 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:50:24,636 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Eigen::Matrix; _Alloc = std::allocator >]’, 2023-09-12T10:50:24,636 inlined from ‘void OpenBabel::QTPIECharges::ParseParamFile()’ at ./src/charges/qtpie.cpp:141:28: 2023-09-12T10:50:24,637 /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 2023-09-12T10:50:24,638 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:50:24,638 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:50:24,887 /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]’: 2023-09-12T10:50:24,887 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:50:24,888 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:50:24,889 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:25,040 /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]’: 2023-09-12T10:50:25,041 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:50:36,725 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:50:36,799 inlined from ‘virtual bool OpenBabel::QTPIECharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qtpie.cpp:330:35: 2023-09-12T10:50:36,808 /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 2023-09-12T10:50:36,812 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:50:36,824 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:50:36,832 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:50:36,833 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, 2023-09-12T10:50:36,834 inlined from ‘virtual bool OpenBabel::QTPIECharges::ComputeCharges(OpenBabel::OBMol&)’ at ./src/charges/qtpie.cpp:331:34: 2023-09-12T10:50:36,835 /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 2023-09-12T10:50:36,836 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:50:36,837 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:40,396 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/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/' 2023-09-12T10:50:40,397 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/ccuAYJDs.s 2023-09-12T10:50:40,402 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:44,375 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/ 2023-09-12T10:50:44,377 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/ 2023-09-12T10:50:44,377 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:50:44,413 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/chiral.cpp -o build/temp.linux-armv7l-cpython-311/./src/chiral.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:50:44,419 Using built-in specs. 2023-09-12T10:50:44,420 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:44,421 Target: arm-linux-gnueabihf 2023-09-12T10:50:44,422 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 2023-09-12T10:50:44,422 Thread model: posix 2023-09-12T10:50:44,423 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:44,424 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:44,425 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:50:44,425 /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/ccpm95JO.s 2023-09-12T10:50:44,438 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:44,439 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:44,441 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:44,441 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:44,442 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:44,443 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:44,443 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:44,444 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:44,445 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:44,446 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:44,447 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:44,448 #include "..." search starts here: 2023-09-12T10:50:44,449 #include <...> search starts here: 2023-09-12T10:50:44,451 /usr/include/eigen3 2023-09-12T10:50:44,453 include 2023-09-12T10:50:44,454 /usr/include/python3.11 2023-09-12T10:50:44,455 /usr/include/c++/12 2023-09-12T10:50:44,456 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:44,457 /usr/include/c++/12/backward 2023-09-12T10:50:44,459 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:44,460 /usr/local/include 2023-09-12T10:50:44,461 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:44,462 /usr/include 2023-09-12T10:50:44,463 End of search list. 2023-09-12T10:50:44,464 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:44,465 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:44,468 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:44,469 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:44,471 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:50:46,053 In file included from include/openbabel/atom.h:33, 2023-09-12T10:50:46,053 from include/openbabel/mol.h:43, 2023-09-12T10:50:46,054 from ./src/chiral.cpp:23: 2023-09-12T10:50:46,055 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:50:46,056 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:50:46,057 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:50:46,057 | ^ 2023-09-12T10:50:46,058 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:46,058 37 | # define UNUSED(x) x 2023-09-12T10:50:46,059 | ^ 2023-09-12T10:50:46,778 In file included from include/openbabel/mol.h:52: 2023-09-12T10:50:46,779 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:46,779 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:46,780 862 | {return new OBVibrationData(*this);} 2023-09-12T10:50:46,781 | ^ 2023-09-12T10:50:46,781 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:50:46,782 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:50:46,782 | ^~~~~~~~ 2023-09-12T10:50:46,783 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:46,784 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:46,785 907 | {return new OBDOSData(*this);} 2023-09-12T10:50:46,785 | ^ 2023-09-12T10:50:46,786 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:50:46,787 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:50:46,788 | ^~~~~~~~ 2023-09-12T10:50:46,802 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:46,803 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:46,804 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:50:46,805 | ^ 2023-09-12T10:50:46,805 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:50:46,806 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:50:46,807 | ^~~~~~~~ 2023-09-12T10:50:46,809 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:46,809 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:46,810 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:50:46,811 | ^ 2023-09-12T10:50:46,812 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:50:46,812 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:50:46,813 | ^~~~~~~~ 2023-09-12T10:50:49,373 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:50:49,374 from include/openbabel/mol.h:35: 2023-09-12T10:50:49,374 /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]’: 2023-09-12T10:50:49,375 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:50:49,375 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:50:49,376 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:50,138 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:50:50,139 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:50:50,140 inlined from ‘double OpenBabel::CalcSignedVolume(OBMol&, OBAtom*, bool)’ at ./src/chiral.cpp:214:27: 2023-09-12T10:50:50,140 /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 2023-09-12T10:50:50,141 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:50:50,141 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:50:50,142 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:50:50,143 inlined from ‘double OpenBabel::CalcSignedVolume(OBMol&, OBAtom*, bool)’ at ./src/chiral.cpp:240:27: 2023-09-12T10:50:50,143 /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 2023-09-12T10:50:50,144 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:50:50,145 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:50:50,739 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/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/' 2023-09-12T10:50:50,740 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/ccpm95JO.s 2023-09-12T10:50:50,747 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:50:50,977 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/ 2023-09-12T10:50:50,978 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/ 2023-09-12T10:50:50,978 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/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.' 2023-09-12T10:50:50,979 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 2023-09-12T10:50:50,985 Using built-in specs. 2023-09-12T10:50:50,985 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:50:50,986 Target: arm-linux-gnueabihf 2023-09-12T10:50:50,987 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 2023-09-12T10:50:50,987 Thread model: posix 2023-09-12T10:50:50,988 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:50:50,988 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:50:50,989 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:50:50,990 /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/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/ccamqBqv.s 2023-09-12T10:50:50,998 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:50,999 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 2023-09-12T10:50:51,000 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:51,001 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:51,001 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:50:51,002 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:50:51,003 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:50:51,004 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:50:51,004 ignoring duplicate directory "/usr/include/" 2023-09-12T10:50:51,005 as it is a non-system directory that duplicates a system directory 2023-09-12T10:50:51,005 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:50:51,006 #include "..." search starts here: 2023-09-12T10:50:51,006 #include <...> search starts here: 2023-09-12T10:50:51,007 /usr/include/eigen3 2023-09-12T10:50:51,007 include 2023-09-12T10:50:51,008 /usr/include/python3.11 2023-09-12T10:50:51,008 /usr/include/c++/12 2023-09-12T10:50:51,009 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:50:51,009 /usr/include/c++/12/backward 2023-09-12T10:50:51,009 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:50:51,010 /usr/local/include 2023-09-12T10:50:51,011 /usr/include/arm-linux-gnueabihf 2023-09-12T10:50:51,011 /usr/include 2023-09-12T10:50:51,011 End of search list. 2023-09-12T10:50:51,012 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:50:51,013 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:50:51,013 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:50:51,014 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:50:51,020 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:50:52,795 In file included from include/openbabel/atom.h:33, 2023-09-12T10:50:52,795 from include/openbabel/mol.h:43, 2023-09-12T10:50:52,796 from include/openbabel/conformersearch.h:24, 2023-09-12T10:50:52,797 from ./src/conformersearch.cpp:20: 2023-09-12T10:50:52,797 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:50:52,798 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:50:52,799 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:50:52,799 | ^ 2023-09-12T10:50:52,800 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:52,801 37 | # define UNUSED(x) x 2023-09-12T10:50:52,802 | ^ 2023-09-12T10:50:53,564 In file included from include/openbabel/mol.h:52: 2023-09-12T10:50:53,565 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:53,566 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:53,566 862 | {return new OBVibrationData(*this);} 2023-09-12T10:50:53,567 | ^ 2023-09-12T10:50:53,568 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:50:53,568 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:50:53,569 | ^~~~~~~~ 2023-09-12T10:50:53,571 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:53,572 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:53,572 907 | {return new OBDOSData(*this);} 2023-09-12T10:50:53,574 | ^ 2023-09-12T10:50:53,574 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:50:53,575 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:50:53,576 | ^~~~~~~~ 2023-09-12T10:50:53,590 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:53,591 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:53,592 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:50:53,592 | ^ 2023-09-12T10:50:53,593 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:50:53,594 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:50:53,594 | ^~~~~~~~ 2023-09-12T10:50:53,597 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:50:53,598 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:50:53,598 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:50:53,599 | ^ 2023-09-12T10:50:53,600 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:50:53,600 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:50:53,601 | ^~~~~~~~ 2023-09-12T10:50:53,805 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:50:53,805 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:50:53,806 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:50:53,807 | ^ 2023-09-12T10:50:53,808 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:53,808 37 | # define UNUSED(x) x 2023-09-12T10:50:53,809 | ^ 2023-09-12T10:50:53,810 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:50:53,810 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:50:53,811 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:50:53,812 | ^ 2023-09-12T10:50:53,812 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:53,813 37 | # define UNUSED(x) x 2023-09-12T10:50:53,814 | ^ 2023-09-12T10:50:55,551 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:50:55,552 from ./src/conformersearch.cpp:22: 2023-09-12T10:50:55,553 include/openbabel/plugin.h: At global scope: 2023-09-12T10:50:55,553 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:50:55,554 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:50:55,555 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:55,555 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:50:55,556 from /usr/include/c++/12/vector:66, 2023-09-12T10:50:55,556 from include/openbabel/mol.h:35: 2023-09-12T10:50:55,557 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:50:55,557 131 | struct binary_function 2023-09-12T10:50:55,558 | ^~~~~~~~~~~~~~~ 2023-09-12T10:50:55,694 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:50:55,694 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,695 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,695 | ^ 2023-09-12T10:50:55,696 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,697 37 | # define UNUSED(x) x 2023-09-12T10:50:55,697 | ^ 2023-09-12T10:50:55,698 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:50:55,699 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,699 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,700 | ^ 2023-09-12T10:50:55,701 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,701 37 | # define UNUSED(x) x 2023-09-12T10:50:55,702 | ^ 2023-09-12T10:50:55,703 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:50:55,703 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,704 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,705 | ^ 2023-09-12T10:50:55,706 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,707 37 | # define UNUSED(x) x 2023-09-12T10:50:55,708 | ^ 2023-09-12T10:50:55,708 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:50:55,709 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,711 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,711 | ^ 2023-09-12T10:50:55,712 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,713 37 | # define UNUSED(x) x 2023-09-12T10:50:55,714 | ^ 2023-09-12T10:50:55,715 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:50:55,716 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,717 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,718 | ^ 2023-09-12T10:50:55,719 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,719 37 | # define UNUSED(x) x 2023-09-12T10:50:55,720 | ^ 2023-09-12T10:50:55,721 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:50:55,722 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,722 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,723 | ^ 2023-09-12T10:50:55,724 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,724 37 | # define UNUSED(x) x 2023-09-12T10:50:55,725 | ^ 2023-09-12T10:50:55,725 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:50:55,726 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,726 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,727 | ^ 2023-09-12T10:50:55,727 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,728 37 | # define UNUSED(x) x 2023-09-12T10:50:55,729 | ^ 2023-09-12T10:50:55,729 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:50:55,730 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:50:55,730 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:50:55,731 | ^ 2023-09-12T10:50:55,732 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:50:55,732 37 | # define UNUSED(x) x 2023-09-12T10:50:55,733 | ^ 2023-09-12T10:50:55,734 ./src/conformersearch.cpp: In member function ‘virtual bool OpenBabel::OBStericConformerFilter::IsGood(const OpenBabel::OBMol&, const OpenBabel::RotorKey&, double*)’: 2023-09-12T10:50:55,734 ./src/conformersearch.cpp:48:74: warning: unused parameter ‘key’ [-Wunused-parameter] 2023-09-12T10:50:55,735 48 | bool OBStericConformerFilter::IsGood(const OBMol &mol, const RotorKey &key, double *conformer) 2023-09-12T10:50:55,736 | ~~~~~~~~~~~~~~~~^~~ 2023-09-12T10:50:55,736 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2023-09-12T10:50:55,737 ./src/conformersearch.cpp:97:55: warning: unused parameter ‘keys’ [-Wunused-parameter] 2023-09-12T10:50:55,738 97 | const RotorKeys &keys, const std::vector &conformers) 2023-09-12T10:50:55,739 | ~~~~~~~~~~~~~~~~~^~~~ 2023-09-12T10:50:55,755 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2023-09-12T10:50:55,756 ./src/conformersearch.cpp:240:12: warning: unused variable ‘score’ [-Wunused-variable] 2023-09-12T10:50:55,757 240 | double score = ff->Energy(false); // no gradients 2023-09-12T10:50:55,757 | ^~~~~ 2023-09-12T10:50:55,758 ./src/conformersearch.cpp:221:65: warning: unused parameter ‘keys’ [-Wunused-parameter] 2023-09-12T10:50:55,759 221 | const RotorKeys &keys, const std::vector &conformers) 2023-09-12T10:50:55,759 | ~~~~~~~~~~~~~~~~~^~~~ 2023-09-12T10:50:55,767 ./src/conformersearch.cpp: In member function ‘bool OpenBabel::OBConformerSearch::Setup(const OpenBabel::OBMol&, int, int, int, int)’: 2023-09-12T10:50:55,768 ./src/conformersearch.cpp:337:23: warning: variable ‘end_it’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:50:55,768 337 | OBRotorIterator end_it = m_rotorList.EndRotors(); 2023-09-12T10:50:55,769 | ^~~~~~ 2023-09-12T10:50:55,836 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::local_opt()’: 2023-09-12T10:50:55,837 ./src/conformersearch.cpp:775:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:50:55,837 775 | for (i = 1; i <= m_rotorList.Size(); ++i, rotor = m_rotorList.NextRotor(ri)) 2023-09-12T10:50:55,838 | ~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:55,843 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::reproduce(OpenBabel::RotorKey&, OpenBabel::RotorKey&)’: 2023-09-12T10:50:55,843 ./src/conformersearch.cpp:836:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:50:55,844 836 | if (iniche > -1) 2023-09-12T10:50:55,844 | ~~~~~~~^~~~ 2023-09-12T10:50:55,858 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::share_fitness()’: 2023-09-12T10:50:55,859 ./src/conformersearch.cpp:991:37: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T10:50:55,859 991 | if ((dynamic_niches.size () < nb_niches) && (dynamic_niches.size () %2)) 2023-09-12T10:50:55,860 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T10:50:55,861 ./src/conformersearch.cpp:1006:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:50:55,861 1006 | if (dist < min_dist ) 2023-09-12T10:50:55,862 | ~~~~~^~~~~~~~~~ 2023-09-12T10:50:55,863 ./src/conformersearch.cpp:1019:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:50:55,863 1019 | if (imax == -1) 2023-09-12T10:50:55,864 | ~~~~~^~~~~ 2023-09-12T10:50:55,865 ./src/conformersearch.cpp:1035:40: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T10:50:55,866 1035 | if (dynamic_niches.size () < nb_niches) 2023-09-12T10:50:55,867 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T10:50:55,867 ./src/conformersearch.cpp:962:10: warning: unused variable ‘flag_niched’ [-Wunused-variable] 2023-09-12T10:50:55,868 962 | bool flag_niched = false; 2023-09-12T10:50:55,869 | ^~~~~~~~~~~ 2023-09-12T10:50:55,877 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::sharing_generation()’: 2023-09-12T10:50:55,877 ./src/conformersearch.cpp:1124:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:50:55,878 1124 | while (ninsert < ((half_pop * 2) / 3)) 2023-09-12T10:50:55,879 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:50:55,879 ./src/conformersearch.cpp:1133:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:50:55,880 1133 | if (iround < imax) 2023-09-12T10:50:55,881 | ~~~~~~~^~~~~~ 2023-09-12T10:50:55,882 ./src/conformersearch.cpp:1141:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:50:55,882 1141 | if (ninsert >= half_pop) 2023-09-12T10:50:55,883 | ~~~~~~~~^~~~~~~~~~~ 2023-09-12T10:50:55,884 ./src/conformersearch.cpp:1166:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:50:55,885 1166 | while (ninsert < half_pop) 2023-09-12T10:50:55,885 | ~~~~~~~~^~~~~~~~~~ 2023-09-12T10:50:55,886 ./src/conformersearch.cpp:1090:23: warning: unused variable ‘lowest’ [-Wunused-variable] 2023-09-12T10:50:55,886 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2023-09-12T10:50:55,887 | ^~~~~~ 2023-09-12T10:50:55,887 ./src/conformersearch.cpp:1090:37: warning: unused variable ‘highest’ [-Wunused-variable] 2023-09-12T10:50:55,888 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2023-09-12T10:50:55,888 | ^~~~~~~ 2023-09-12T10:50:59,970 In file included from /usr/include/c++/12/algorithm:61, 2023-09-12T10:50:59,970 from include/openbabel/ring.h:24, 2023-09-12T10:50:59,971 from include/openbabel/mol.h:51: 2023-09-12T10:50:59,971 /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]’: 2023-09-12T10:50:59,972 /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 2023-09-12T10:50:59,972 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, 2023-09-12T10:50:59,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:00,039 /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]’: 2023-09-12T10:51:00,040 /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 2023-09-12T10:51:00,041 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:51:00,042 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:51:00,043 /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 2023-09-12T10:51:00,101 /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]’: 2023-09-12T10:51:00,102 /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 2023-09-12T10:51:00,102 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, 2023-09-12T10:51:00,103 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:00,169 /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]’: 2023-09-12T10:51:00,169 /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 2023-09-12T10:51:00,170 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:51:00,171 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:51:00,172 /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 2023-09-12T10:51:00,252 In file included from /usr/include/c++/12/bits/stl_algo.h:60: 2023-09-12T10:51:00,252 /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]’: 2023-09-12T10:51:00,253 /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 2023-09-12T10:51:00,253 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T10:51:00,254 | ^~~~~~~~~~~~~ 2023-09-12T10:51:00,521 /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]’: 2023-09-12T10:51:00,521 /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 2023-09-12T10:51:01,583 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:51:01,584 /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]’: 2023-09-12T10:51:01,585 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:01,586 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:01,586 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:01,984 /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]’: 2023-09-12T10:51:01,985 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:02,134 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:51:02,134 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, 2023-09-12T10:51:02,135 inlined from ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:249:19: 2023-09-12T10:51:02,136 /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 2023-09-12T10:51:02,137 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:02,137 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,138 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:51:02,139 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, 2023-09-12T10:51:02,139 inlined from ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:262:21: 2023-09-12T10:51:02,140 /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 2023-09-12T10:51:02,140 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:02,141 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,365 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:51:02,366 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, 2023-09-12T10:51:02,367 inlined from ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:105:19: 2023-09-12T10:51:02,367 /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 2023-09-12T10:51:02,368 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:02,369 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,369 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:51:02,370 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, 2023-09-12T10:51:02,371 inlined from ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’ at ./src/conformersearch.cpp:118:21: 2023-09-12T10:51:02,372 /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 2023-09-12T10:51:02,372 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:02,373 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,502 /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]’: 2023-09-12T10:51:02,503 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:02,504 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:02,504 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,671 /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]’: 2023-09-12T10:51:02,672 /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 2023-09-12T10:51:02,672 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:51:02,673 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,674 /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 2023-09-12T10:51:02,676 /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 2023-09-12T10:51:02,676 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:51:02,677 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,955 /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]’: 2023-09-12T10:51:02,956 /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 2023-09-12T10:51:02,957 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:51:02,957 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:51:02,958 /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 2023-09-12T10:51:02,960 /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 2023-09-12T10:51:02,961 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:51:02,961 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,135 /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]’: 2023-09-12T10:51:03,135 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:03,136 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:03,137 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,298 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:03,299 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, 2023-09-12T10:51:03,299 inlined from ‘int OpenBabel::OBConformerSearch::share_fitness()’ at ./src/conformersearch.cpp:979:34: 2023-09-12T10:51:03,300 /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 2023-09-12T10:51:03,301 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:03,302 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,302 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:03,303 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, 2023-09-12T10:51:03,303 inlined from ‘int OpenBabel::OBConformerSearch::share_fitness()’ at ./src/conformersearch.cpp:982:34: 2023-09-12T10:51:03,304 /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 2023-09-12T10:51:03,304 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:03,305 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,977 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::ConformerScore}; _Tp = OpenBabel::ConformerScore; _Alloc = std::allocator]’, 2023-09-12T10:51:03,978 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, 2023-09-12T10:51:03,979 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:927:35: 2023-09-12T10:51:03,979 /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 2023-09-12T10:51:03,980 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:03,981 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,982 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:03,982 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, 2023-09-12T10:51:03,983 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2023-09-12T10:51:03,984 /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 2023-09-12T10:51:03,985 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:51:03,985 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,986 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:51:03,987 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,987 1939 | __comp); 2023-09-12T10:51:03,988 | ~~~~~~~ 2023-09-12T10:51:03,989 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:03,990 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, 2023-09-12T10:51:03,991 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, 2023-09-12T10:51:03,991 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2023-09-12T10:51:03,992 /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 2023-09-12T10:51:03,992 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:51:03,993 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,993 /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 2023-09-12T10:51:03,994 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:51:03,994 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,995 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:03,996 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, 2023-09-12T10:51:03,996 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2023-09-12T10:51:03,997 /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 2023-09-12T10:51:03,998 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:51:03,998 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:51:03,999 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:51:04,000 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,000 1939 | __comp); 2023-09-12T10:51:04,001 | ~~~~~~~ 2023-09-12T10:51:04,002 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:04,002 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, 2023-09-12T10:51:04,003 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, 2023-09-12T10:51:04,003 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2023-09-12T10:51:04,004 /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 2023-09-12T10:51:04,005 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:51:04,005 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,006 /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 2023-09-12T10:51:04,006 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:51:04,007 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,008 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:51:04,008 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:04,009 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:946:27: 2023-09-12T10:51:04,009 /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 2023-09-12T10:51:04,010 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:04,011 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:04,441 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::MakeSelection()’: 2023-09-12T10:51:04,442 ./src/conformersearch.cpp:535:31: warning: ‘highest’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:51:04,442 535 | double sum = 0.0, lowest, highest; 2023-09-12T10:51:04,443 | ^~~~~~~ 2023-09-12T10:51:04,453 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::ConformerScore}; _Tp = OpenBabel::ConformerScore; _Alloc = std::allocator]’, 2023-09-12T10:51:04,454 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, 2023-09-12T10:51:04,455 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:516:33: 2023-09-12T10:51:04,456 /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 2023-09-12T10:51:04,456 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:04,457 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,458 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:04,458 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, 2023-09-12T10:51:04,459 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2023-09-12T10:51:04,460 /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 2023-09-12T10:51:04,461 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:51:04,461 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,462 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:51:04,462 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,463 1939 | __comp); 2023-09-12T10:51:04,463 | ~~~~~~~ 2023-09-12T10:51:04,464 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:04,464 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, 2023-09-12T10:51:04,465 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, 2023-09-12T10:51:04,466 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2023-09-12T10:51:04,466 /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 2023-09-12T10:51:04,467 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:51:04,468 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,468 /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 2023-09-12T10:51:04,469 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:51:04,470 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,471 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:04,472 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, 2023-09-12T10:51:04,472 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2023-09-12T10:51:04,473 /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 2023-09-12T10:51:04,474 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:51:04,474 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,475 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:51:04,476 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,477 1939 | __comp); 2023-09-12T10:51:04,477 | ~~~~~~~ 2023-09-12T10:51:04,477 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2023-09-12T10:51:04,478 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, 2023-09-12T10:51:04,478 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, 2023-09-12T10:51:04,479 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2023-09-12T10:51:04,479 /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 2023-09-12T10:51:04,480 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:51:04,480 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:04,481 /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 2023-09-12T10:51:04,482 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:51:04,483 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:06,267 In file included from /usr/include/c++/12/map:60, 2023-09-12T10:51:06,267 from include/openbabel/mol.h:37: 2023-09-12T10:51:06,268 /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> >]’: 2023-09-12T10:51:06,269 /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 2023-09-12T10:51:06,270 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T10:51:06,270 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:08,830 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:08,831 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/ccamqBqv.s 2023-09-12T10:51:08,836 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:51:09,947 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/ 2023-09-12T10:51:09,948 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/ 2023-09-12T10:51:09,948 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:51:09,953 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 2023-09-12T10:51:09,957 Using built-in specs. 2023-09-12T10:51:09,958 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:51:09,959 Target: arm-linux-gnueabihf 2023-09-12T10:51:09,960 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 2023-09-12T10:51:09,960 Thread model: posix 2023-09-12T10:51:09,961 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:51:09,961 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:51:09,962 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:09,963 /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/ccbQONFb.s 2023-09-12T10:51:09,970 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:09,971 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:09,972 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:09,973 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:09,973 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:51:09,974 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:51:09,974 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:51:09,975 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:51:09,975 ignoring duplicate directory "/usr/include/" 2023-09-12T10:51:09,976 as it is a non-system directory that duplicates a system directory 2023-09-12T10:51:09,976 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:51:09,977 #include "..." search starts here: 2023-09-12T10:51:09,977 #include <...> search starts here: 2023-09-12T10:51:09,978 /usr/include/eigen3 2023-09-12T10:51:09,978 include 2023-09-12T10:51:09,979 /usr/include/python3.11 2023-09-12T10:51:09,979 /usr/include/c++/12 2023-09-12T10:51:09,980 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:09,980 /usr/include/c++/12/backward 2023-09-12T10:51:09,981 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:09,982 /usr/local/include 2023-09-12T10:51:09,982 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:09,983 /usr/include 2023-09-12T10:51:09,984 End of search list. 2023-09-12T10:51:09,985 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:09,985 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 2023-09-12T10:51:09,987 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:09,988 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:09,988 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:11,746 In file included from include/openbabel/forcefield.h:30, 2023-09-12T10:51:11,747 from ./src/confsearch.cpp:23: 2023-09-12T10:51:11,748 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:51:11,748 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:51:11,749 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:51:11,750 | ^ 2023-09-12T10:51:11,750 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:11,751 37 | # define UNUSED(x) x 2023-09-12T10:51:11,751 | ^ 2023-09-12T10:51:12,552 In file included from include/openbabel/mol.h:52, 2023-09-12T10:51:12,553 from include/openbabel/forcefield.h:31: 2023-09-12T10:51:12,553 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:12,554 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:12,555 862 | {return new OBVibrationData(*this);} 2023-09-12T10:51:12,556 | ^ 2023-09-12T10:51:12,556 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:51:12,557 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:51:12,558 | ^~~~~~~~ 2023-09-12T10:51:12,558 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:12,559 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:12,559 907 | {return new OBDOSData(*this);} 2023-09-12T10:51:12,560 | ^ 2023-09-12T10:51:12,560 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:51:12,561 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:51:12,562 | ^~~~~~~~ 2023-09-12T10:51:12,576 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:12,577 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:12,578 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:51:12,578 | ^ 2023-09-12T10:51:12,579 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:51:12,580 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:51:12,580 | ^~~~~~~~ 2023-09-12T10:51:12,583 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:12,583 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:12,584 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:51:12,585 | ^ 2023-09-12T10:51:12,586 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:51:12,586 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:51:12,587 | ^~~~~~~~ 2023-09-12T10:51:12,756 In file included from include/openbabel/forcefield.h:32: 2023-09-12T10:51:12,756 include/openbabel/plugin.h: At global scope: 2023-09-12T10:51:12,757 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:51:12,758 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:51:12,759 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:12,759 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:51:12,760 from /usr/include/c++/12/vector:66, 2023-09-12T10:51:12,761 from include/openbabel/forcefield.h:23: 2023-09-12T10:51:12,762 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:51:12,762 131 | struct binary_function 2023-09-12T10:51:12,763 | ^~~~~~~~~~~~~~~ 2023-09-12T10:51:12,882 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:51:12,883 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,883 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,884 | ^ 2023-09-12T10:51:12,884 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,885 37 | # define UNUSED(x) x 2023-09-12T10:51:12,886 | ^ 2023-09-12T10:51:12,886 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:51:12,887 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,888 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,888 | ^ 2023-09-12T10:51:12,889 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,889 37 | # define UNUSED(x) x 2023-09-12T10:51:12,890 | ^ 2023-09-12T10:51:12,891 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:51:12,891 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,892 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,893 | ^ 2023-09-12T10:51:12,893 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,894 37 | # define UNUSED(x) x 2023-09-12T10:51:12,895 | ^ 2023-09-12T10:51:12,895 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:51:12,896 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,897 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,898 | ^ 2023-09-12T10:51:12,898 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,899 37 | # define UNUSED(x) x 2023-09-12T10:51:12,900 | ^ 2023-09-12T10:51:12,901 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:51:12,901 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,902 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,903 | ^ 2023-09-12T10:51:12,903 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,904 37 | # define UNUSED(x) x 2023-09-12T10:51:12,905 | ^ 2023-09-12T10:51:12,905 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:51:12,906 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,907 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,908 | ^ 2023-09-12T10:51:12,908 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,909 37 | # define UNUSED(x) x 2023-09-12T10:51:12,910 | ^ 2023-09-12T10:51:12,910 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:51:12,911 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,911 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,912 | ^ 2023-09-12T10:51:12,912 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,913 37 | # define UNUSED(x) x 2023-09-12T10:51:12,914 | ^ 2023-09-12T10:51:12,914 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:51:12,915 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:51:12,915 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:51:12,916 | ^ 2023-09-12T10:51:12,917 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,917 37 | # define UNUSED(x) x 2023-09-12T10:51:12,918 | ^ 2023-09-12T10:51:12,932 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:51:12,932 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:51:12,933 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:51:12,934 | ^ 2023-09-12T10:51:12,934 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,935 37 | # define UNUSED(x) x 2023-09-12T10:51:12,936 | ^ 2023-09-12T10:51:12,937 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:51:12,937 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:51:12,938 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:51:12,938 | ^ 2023-09-12T10:51:12,939 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:12,940 37 | # define UNUSED(x) x 2023-09-12T10:51:12,940 | ^ 2023-09-12T10:51:15,000 ./src/confsearch.cpp: In member function ‘unsigned int OpenBabel::LFSR::GetNext()’: 2023-09-12T10:51:15,001 ./src/confsearch.cpp:86:47: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 2023-09-12T10:51:15,001 86 | _lfsr = (_lfsr >> 1) ^ (unsigned int)(0 - (_lfsr & 1u) & _poly); 2023-09-12T10:51:15,002 | ~~^~~~~~~~~~~~~~ 2023-09-12T10:51:15,012 ./src/confsearch.cpp: In constructor ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’: 2023-09-12T10:51:15,013 ./src/confsearch.cpp:125:20: warning: ‘OpenBabel::OBDiversePoses::cutoff’ will be initialized after [-Wreorder] 2023-09-12T10:51:15,013 125 | const double cutoff; 2023-09-12T10:51:15,014 | ^~~~~~ 2023-09-12T10:51:15,015 ./src/confsearch.cpp:119:12: warning: ‘bool OpenBabel::OBDiversePoses::_percise’ [-Wreorder] 2023-09-12T10:51:15,016 119 | bool _percise; 2023-09-12T10:51:15,016 | ^~~~~~~~ 2023-09-12T10:51:15,017 ./src/confsearch.cpp:139:3: warning: when initialized here [-Wreorder] 2023-09-12T10:51:15,018 139 | OBDiversePoses::OBDiversePoses(const OBMol &ref, double RMSD, bool percise): 2023-09-12T10:51:15,019 | ^~~~~~~~~~~~~~ 2023-09-12T10:51:15,020 ./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] 2023-09-12T10:51:15,020 149 | vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less(), (cutoff + 0.1) )), vec.end()); 2023-09-12T10:51:15,021 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:15,022 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T10:51:15,022 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T10:51:15,023 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T10:51:15,023 | ^~~~~~~ 2023-09-12T10:51:15,029 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(double*, double, int)’: 2023-09-12T10:51:15,030 ./src/confsearch.cpp:166:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:51:15,030 166 | for (unsigned int a = 0; a < natoms; ++a) 2023-09-12T10:51:15,031 | ~~^~~~~~~~ 2023-09-12T10:51:15,066 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’: 2023-09-12T10:51:15,067 ./src/confsearch.cpp:205:14: warning: unused variable ‘min_rmsd’ [-Wunused-variable] 2023-09-12T10:51:15,068 205 | double min_rmsd = DBL_MAX; 2023-09-12T10:51:15,068 | ^~~~~~~~ 2023-09-12T10:51:15,071 ./src/confsearch.cpp:269:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:51:15,072 269 | for (int k = *c; k < levels.size(); ++k) { 2023-09-12T10:51:15,072 | ~~^~~~~~~~~~~~~~~ 2023-09-12T10:51:15,073 ./src/confsearch.cpp: In member function ‘std::vector OpenBabel::OBDiversePoses::GetHeavyAtomCoords(const std::vector&)’: 2023-09-12T10:51:15,074 ./src/confsearch.cpp:283:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:51:15,075 283 | for (unsigned int a = 0; a < natoms; ++a) 2023-09-12T10:51:15,076 | ~~^~~~~~~~ 2023-09-12T10:51:15,094 ./src/confsearch.cpp: In member function ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’: 2023-09-12T10:51:15,095 ./src/confsearch.cpp:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:51:15,096 426 | for (int i = 1; i < rl.Size() + 1; ++i, rotor = rl.NextRotor(ri)) { // foreach rotor 2023-09-12T10:51:15,096 | ~~^~~~~~~~~~~~~~~ 2023-09-12T10:51:15,107 ./src/confsearch.cpp:464:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:51:15,107 464 | for (int i = 0 ; i < rotor_sizes.size(); ++i) { 2023-09-12T10:51:15,108 | ~~^~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:15,109 ./src/confsearch.cpp:479:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:51:15,110 479 | } while (combination != 1 && counter < nconfs); // The LFSR always terminates with a 1 2023-09-12T10:51:15,110 | ~~~~~~~~^~~~~~~~ 2023-09-12T10:51:15,112 ./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] 2023-09-12T10:51:15,113 489 | transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(plus(), energy_offset)); 2023-09-12T10:51:15,114 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:15,115 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T10:51:15,116 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T10:51:15,116 | ^~~~~~~ 2023-09-12T10:51:15,117 ./src/confsearch.cpp:402:9: warning: unused variable ‘origLogLevel’ [-Wunused-variable] 2023-09-12T10:51:15,117 402 | int origLogLevel = _loglvl; 2023-09-12T10:51:15,118 | ^~~~~~~~~~~~ 2023-09-12T10:51:20,807 In file included from /usr/include/c++/12/vector:60: 2023-09-12T10:51:20,808 /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 > >]’: 2023-09-12T10:51:20,808 /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 2023-09-12T10:51:20,809 2131 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, 2023-09-12T10:51:20,809 | ^~~~~~~~~~~ 2023-09-12T10:51:20,810 /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 2023-09-12T10:51:20,853 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:51:20,853 /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]’: 2023-09-12T10:51:20,854 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:20,855 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:20,855 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:20,983 In file included from /usr/include/c++/12/algorithm:61, 2023-09-12T10:51:20,983 from include/openbabel/ring.h:24, 2023-09-12T10:51:20,984 from include/openbabel/mol.h:51: 2023-09-12T10:51:20,985 In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator >; _Predicate = binder2nd >]’, 2023-09-12T10:51:20,986 inlined from ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’ at ./src/confsearch.cpp:149:29: 2023-09-12T10:51:20,986 /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 2023-09-12T10:51:20,987 877 | return std::__remove_if(__first, __last, 2023-09-12T10:51:20,988 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:51:20,989 878 | __gnu_cxx::__ops::__pred_iter(__pred)); 2023-09-12T10:51:20,989 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:20,990 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:51:20,991 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:20,992 inlined from ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’ at ./src/confsearch.cpp:150:18: 2023-09-12T10:51:20,992 /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 2023-09-12T10:51:20,993 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:20,994 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:21,246 /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]’: 2023-09-12T10:51:21,247 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:21,248 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:21,248 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:21,302 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:51:21,302 inlined from ‘std::vector OpenBabel::GetHeavyAtomCoords(const OBMol*, const std::vector&)’ at ./src/confsearch.cpp:302:27: 2023-09-12T10:51:21,303 /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 2023-09-12T10:51:21,304 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:21,304 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:21,338 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:51:21,339 inlined from ‘std::vector OpenBabel::OBDiversePoses::GetHeavyAtomCoords(const std::vector&)’ at ./src/confsearch.cpp:285:29: 2023-09-12T10:51:21,340 /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 2023-09-12T10:51:21,340 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:21,341 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:21,414 /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> >]’: 2023-09-12T10:51:21,415 /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 2023-09-12T10:51:21,416 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:21,416 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:21,716 /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]’: 2023-09-12T10:51:21,717 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:21,846 /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> >]’: 2023-09-12T10:51:21,847 /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 2023-09-12T10:51:22,142 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:22,143 inlined from ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’ at ./src/confsearch.cpp:225:36: 2023-09-12T10:51:22,143 /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 2023-09-12T10:51:22,144 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:22,145 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:22,145 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> >]’, 2023-09-12T10:51:22,146 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, 2023-09-12T10:51:22,146 inlined from ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’ at ./src/confsearch.cpp:240:30: 2023-09-12T10:51:22,147 /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 2023-09-12T10:51:22,148 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:22,148 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:22,578 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:51:22,578 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, 2023-09-12T10:51:22,579 inlined from ‘bool OpenBabel::OBDiversePoses::AddPose(double*, double, int)’ at ./src/confsearch.cpp:167:24: 2023-09-12T10:51:22,580 /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 2023-09-12T10:51:22,581 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:22,581 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:22,664 /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]’: 2023-09-12T10:51:22,664 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:22,665 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:22,666 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:22,833 /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>&)>]’: 2023-09-12T10:51:22,834 /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 2023-09-12T10:51:22,835 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, 2023-09-12T10:51:22,836 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:22,909 /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>&)>]’: 2023-09-12T10:51:22,909 /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 2023-09-12T10:51:22,910 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:51:22,911 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:51:22,911 /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 2023-09-12T10:51:22,995 In file included from /usr/include/c++/12/bits/stl_algo.h:60: 2023-09-12T10:51:22,996 /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>&)>]’: 2023-09-12T10:51:22,997 /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 2023-09-12T10:51:22,998 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T10:51:22,998 | ^~~~~~~~~~~~~ 2023-09-12T10:51:23,107 /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>&)>]’: 2023-09-12T10:51:23,108 /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 2023-09-12T10:51:23,109 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, 2023-09-12T10:51:23,110 | ^~~~~~~~~~~ 2023-09-12T10:51:23,110 /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 2023-09-12T10:51:23,248 /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>&)>]’: 2023-09-12T10:51:23,249 /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 2023-09-12T10:51:23,249 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:51:23,250 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:51:23,250 /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 2023-09-12T10:51:23,252 /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 2023-09-12T10:51:23,252 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:51:23,253 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:23,254 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>&)>]’, 2023-09-12T10:51:23,255 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, 2023-09-12T10:51:23,256 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: 2023-09-12T10:51:23,256 /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 2023-09-12T10:51:23,257 1629 | std::__make_heap(__first, __middle, __comp); 2023-09-12T10:51:23,258 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:23,600 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’, 2023-09-12T10:51:23,601 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:318:22: 2023-09-12T10:51:23,601 /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 2023-09-12T10:51:23,602 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:23,603 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:23,603 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>&)>]’, 2023-09-12T10:51:23,604 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, 2023-09-12T10:51:23,604 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2023-09-12T10:51:23,605 /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 2023-09-12T10:51:23,606 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:51:23,607 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:51:23,607 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:51:23,608 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:23,609 1939 | __comp); 2023-09-12T10:51:23,610 | ~~~~~~~ 2023-09-12T10:51:23,610 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>&)>]’, 2023-09-12T10:51:23,611 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, 2023-09-12T10:51:23,612 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, 2023-09-12T10:51:23,613 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2023-09-12T10:51:23,613 /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 2023-09-12T10:51:23,614 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:51:23,614 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:23,615 /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 2023-09-12T10:51:23,616 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:51:23,616 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:23,617 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::triple, double, int>; _Alloc = std::allocator, double, int> >]’, 2023-09-12T10:51:23,618 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:334:25: 2023-09-12T10:51:23,619 /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 2023-09-12T10:51:23,619 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:23,620 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:23,621 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:23,622 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:363:25: 2023-09-12T10:51:23,622 /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 2023-09-12T10:51:23,623 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:23,624 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:24,197 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:24,198 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, 2023-09-12T10:51:24,199 inlined from ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’ at ./src/confsearch.cpp:393:26: 2023-09-12T10:51:24,200 /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 2023-09-12T10:51:24,200 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:24,201 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:24,201 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:24,202 inlined from ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’ at ./src/confsearch.cpp:420:24: 2023-09-12T10:51:24,202 /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 2023-09-12T10:51:24,203 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:24,203 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:26,171 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:26,172 inlined from ‘int OpenBabel::OBForceField::ScreenByRMSD(double, double, short int, OpenBabel::OBBitVec, bool)’ at ./src/confsearch.cpp:669:28: 2023-09-12T10:51:26,172 /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 2023-09-12T10:51:26,173 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:26,174 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:26,175 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:26,175 inlined from ‘int OpenBabel::OBForceField::ScreenByRMSD(double, double, short int, OpenBabel::OBBitVec, bool)’ at ./src/confsearch.cpp:679:32: 2023-09-12T10:51:26,176 /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 2023-09-12T10:51:26,177 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:26,178 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:27,527 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:27,527 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/ccbQONFb.s 2023-09-12T10:51:27,532 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:51:28,465 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/ 2023-09-12T10:51:28,465 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/ 2023-09-12T10:51:28,466 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/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.' 2023-09-12T10:51:28,471 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 2023-09-12T10:51:28,475 Using built-in specs. 2023-09-12T10:51:28,478 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:51:28,479 Target: arm-linux-gnueabihf 2023-09-12T10:51:28,479 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 2023-09-12T10:51:28,480 Thread model: posix 2023-09-12T10:51:28,480 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:51:28,481 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:51:28,481 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:28,482 /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/ccSwXpTw.s 2023-09-12T10:51:28,489 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:28,490 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 2023-09-12T10:51:28,491 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:28,492 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:28,493 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:51:28,493 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:51:28,494 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:51:28,495 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:51:28,495 ignoring duplicate directory "/usr/include/" 2023-09-12T10:51:28,496 as it is a non-system directory that duplicates a system directory 2023-09-12T10:51:28,496 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:51:28,496 #include "..." search starts here: 2023-09-12T10:51:28,497 #include <...> search starts here: 2023-09-12T10:51:28,497 /usr/include/eigen3 2023-09-12T10:51:28,498 include 2023-09-12T10:51:28,498 /usr/include/python3.11 2023-09-12T10:51:28,499 /usr/include/c++/12 2023-09-12T10:51:28,499 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:28,500 /usr/include/c++/12/backward 2023-09-12T10:51:28,500 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:28,500 /usr/local/include 2023-09-12T10:51:28,501 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:28,501 /usr/include 2023-09-12T10:51:28,502 End of search list. 2023-09-12T10:51:28,502 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:28,503 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:28,503 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:28,504 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:28,515 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:30,234 In file included from include/openbabel/atom.h:33, 2023-09-12T10:51:30,234 from include/openbabel/mol.h:43, 2023-09-12T10:51:30,235 from include/openbabel/data_utilities.h:25, 2023-09-12T10:51:30,236 from ./src/data.cpp:22: 2023-09-12T10:51:30,236 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:51:30,237 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:51:30,238 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:51:30,238 | ^ 2023-09-12T10:51:30,239 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:30,240 37 | # define UNUSED(x) x 2023-09-12T10:51:30,241 | ^ 2023-09-12T10:51:30,910 In file included from include/openbabel/mol.h:52: 2023-09-12T10:51:30,911 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:30,912 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:30,912 862 | {return new OBVibrationData(*this);} 2023-09-12T10:51:30,913 | ^ 2023-09-12T10:51:30,913 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:51:30,914 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:51:30,915 | ^~~~~~~~ 2023-09-12T10:51:30,919 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:30,920 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:30,920 907 | {return new OBDOSData(*this);} 2023-09-12T10:51:30,921 | ^ 2023-09-12T10:51:30,922 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:51:30,922 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:51:30,923 | ^~~~~~~~ 2023-09-12T10:51:30,941 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:30,941 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:30,942 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:51:30,942 | ^ 2023-09-12T10:51:30,943 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:51:30,943 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:51:30,944 | ^~~~~~~~ 2023-09-12T10:51:30,950 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:30,950 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:30,951 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:51:30,952 | ^ 2023-09-12T10:51:30,952 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:51:30,953 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:51:30,953 | ^~~~~~~~ 2023-09-12T10:51:31,695 ./src/data.cpp: In member function ‘bool OpenBabel::OBResidueData::AssignBonds(OpenBabel::OBMol&, OpenBabel::OBBitVec&)’: 2023-09-12T10:51:31,695 ./src/data.cpp:810:56: warning: unused parameter ‘bv’ [-Wunused-parameter] 2023-09-12T10:51:31,696 810 | bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &bv) 2023-09-12T10:51:31,697 | ~~~~~~~~~~^~ 2023-09-12T10:51:38,734 In file included from ./src/data.cpp:21: 2023-09-12T10:51:38,735 In constructor ‘OpenBabel::OBElement::OBElement(int, const char*, double, double, double, int, double, double, double, double, double, double, double, std::string)’, 2023-09-12T10:51:38,735 inlined from ‘virtual void OpenBabel::OBElementTable::ParseLine(const char*)’ at ./src/data.cpp:117:79: 2023-09-12T10:51:38,736 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] 2023-09-12T10:51:38,737 118 | strncpy(_symbol, sym, 3); // Make sure to leave 4th character for null 2023-09-12T10:51:38,737 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:51:38,829 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:51:38,830 from include/openbabel/data.h:28: 2023-09-12T10:51:38,830 /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 >]’: 2023-09-12T10:51:38,831 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:51:38,832 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:38,833 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:39,090 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:51:39,091 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:51:39,092 inlined from ‘virtual void OpenBabel::OBIsotopeTable::ParseLine(const char*)’ at ./src/data.cpp:393:30: 2023-09-12T10:51:39,092 /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 2023-09-12T10:51:39,092 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:39,093 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:39,220 /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]’: 2023-09-12T10:51:39,221 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:39,221 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:39,222 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:39,282 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:39,282 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, 2023-09-12T10:51:39,283 inlined from ‘std::vector OpenBabel::OBElementTable::GetRGB(int)’ at ./src/data.cpp:210:25: 2023-09-12T10:51:39,284 /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 2023-09-12T10:51:39,285 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:39,286 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:39,287 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:39,288 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, 2023-09-12T10:51:39,288 inlined from ‘std::vector OpenBabel::OBElementTable::GetRGB(int)’ at ./src/data.cpp:216:21: 2023-09-12T10:51:39,289 /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 2023-09-12T10:51:39,289 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:51:39,290 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:41,149 /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]’: 2023-09-12T10:51:41,149 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:41,150 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:41,151 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:41,396 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBAtomHOF; _Alloc = std::allocator]’, 2023-09-12T10:51:41,397 inlined from ‘virtual void OpenBabel::OBAtomicHeatOfFormationTable::ParseLine(const char*)’ at ./src/data.cpp:490:31: 2023-09-12T10:51:41,398 /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 2023-09-12T10:51:41,398 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:41,399 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:42,153 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:42,153 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/ccSwXpTw.s 2023-09-12T10:51:42,158 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:51:43,215 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/ 2023-09-12T10:51:43,215 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/ 2023-09-12T10:51:43,216 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/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.' 2023-09-12T10:51:43,220 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 2023-09-12T10:51:43,224 Using built-in specs. 2023-09-12T10:51:43,225 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:51:43,226 Target: arm-linux-gnueabihf 2023-09-12T10:51:43,226 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 2023-09-12T10:51:43,227 Thread model: posix 2023-09-12T10:51:43,228 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:51:43,228 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:51:43,229 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:43,229 /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/ccqiqM0d.s 2023-09-12T10:51:43,237 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:43,238 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:43,239 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:43,240 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:43,240 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:51:43,241 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:51:43,242 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:51:43,242 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:51:43,243 ignoring duplicate directory "/usr/include/" 2023-09-12T10:51:43,243 as it is a non-system directory that duplicates a system directory 2023-09-12T10:51:43,244 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:51:43,244 #include "..." search starts here: 2023-09-12T10:51:43,245 #include <...> search starts here: 2023-09-12T10:51:43,246 /usr/include/eigen3 2023-09-12T10:51:43,246 include 2023-09-12T10:51:43,247 /usr/include/python3.11 2023-09-12T10:51:43,247 /usr/include/c++/12 2023-09-12T10:51:43,248 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:43,249 /usr/include/c++/12/backward 2023-09-12T10:51:43,249 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:43,250 /usr/local/include 2023-09-12T10:51:43,250 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:43,251 /usr/include 2023-09-12T10:51:43,252 End of search list. 2023-09-12T10:51:43,252 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:43,253 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:43,254 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:43,255 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:43,256 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:44,797 In file included from include/openbabel/atom.h:33, 2023-09-12T10:51:44,797 from include/openbabel/mol.h:43, 2023-09-12T10:51:44,798 from include/openbabel/data_utilities.h:25, 2023-09-12T10:51:44,798 from ./src/data_utilities.cpp:23: 2023-09-12T10:51:44,799 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:51:44,799 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:51:44,800 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:51:44,800 | ^ 2023-09-12T10:51:44,801 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:44,802 37 | # define UNUSED(x) x 2023-09-12T10:51:44,802 | ^ 2023-09-12T10:51:45,563 In file included from include/openbabel/mol.h:52: 2023-09-12T10:51:45,564 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:45,564 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:45,565 862 | {return new OBVibrationData(*this);} 2023-09-12T10:51:45,566 | ^ 2023-09-12T10:51:45,566 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:51:45,567 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:51:45,568 | ^~~~~~~~ 2023-09-12T10:51:45,569 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:45,569 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:45,570 907 | {return new OBDOSData(*this);} 2023-09-12T10:51:45,571 | ^ 2023-09-12T10:51:45,572 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:51:45,572 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:51:45,573 | ^~~~~~~~ 2023-09-12T10:51:45,587 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:45,588 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:45,589 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:51:45,589 | ^ 2023-09-12T10:51:45,590 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:51:45,591 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:51:45,592 | ^~~~~~~~ 2023-09-12T10:51:45,594 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:45,595 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:45,596 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:51:45,596 | ^ 2023-09-12T10:51:45,597 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:51:45,597 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:51:45,598 | ^~~~~~~~ 2023-09-12T10:51:45,897 ./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&)’: 2023-09-12T10:51:45,897 ./src/data_utilities.cpp:121:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:51:45,898 121 | for(int i = 0; (i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-12T10:51:47,278 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:51:47,278 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:51:47,279 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:51:47,464 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:51:47,465 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:47,466 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: 2023-09-12T10:51:47,467 /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 2023-09-12T10:51:47,467 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:47,468 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:47,469 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:47,470 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: 2023-09-12T10:51:47,470 /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 2023-09-12T10:51:47,471 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:47,472 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:47,473 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:47,473 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: 2023-09-12T10:51:47,474 /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 2023-09-12T10:51:47,476 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:47,476 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:47,477 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:47,477 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: 2023-09-12T10:51:47,478 /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 2023-09-12T10:51:47,478 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:47,479 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:47,479 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:51:47,480 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: 2023-09-12T10:51:47,480 /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 2023-09-12T10:51:47,481 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:51:47,481 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:47,809 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/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/' 2023-09-12T10:51:47,810 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/ccqiqM0d.s 2023-09-12T10:51:47,816 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:51:47,904 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/ 2023-09-12T10:51:47,905 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/ 2023-09-12T10:51:47,905 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/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.' 2023-09-12T10:51:47,906 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 2023-09-12T10:51:47,911 Using built-in specs. 2023-09-12T10:51:47,911 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:51:47,912 Target: arm-linux-gnueabihf 2023-09-12T10:51:47,912 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 2023-09-12T10:51:47,913 Thread model: posix 2023-09-12T10:51:47,913 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:51:47,914 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:51:47,914 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:47,915 /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/ccNHeaBa.s 2023-09-12T10:51:47,924 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:47,924 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:47,926 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:47,926 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:47,927 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:51:47,927 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:51:47,928 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:51:47,929 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:51:47,929 ignoring duplicate directory "/usr/include/" 2023-09-12T10:51:47,930 as it is a non-system directory that duplicates a system directory 2023-09-12T10:51:47,931 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:51:47,932 #include "..." search starts here: 2023-09-12T10:51:47,932 #include <...> search starts here: 2023-09-12T10:51:47,933 /usr/include/eigen3 2023-09-12T10:51:47,933 include 2023-09-12T10:51:47,933 /usr/include/python3.11 2023-09-12T10:51:47,934 /usr/include/c++/12 2023-09-12T10:51:47,934 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:47,935 /usr/include/c++/12/backward 2023-09-12T10:51:47,935 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:47,936 /usr/local/include 2023-09-12T10:51:47,936 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:47,937 /usr/include 2023-09-12T10:51:47,937 End of search list. 2023-09-12T10:51:47,937 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:47,938 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:47,939 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:47,939 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:47,941 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:49,187 In file included from ./src/depict/asciipainter.cpp:19: 2023-09-12T10:51:49,187 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2023-09-12T10:51:49,188 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T10:51:49,188 34 | void SetFontFamily(const std::string &fontFamily) {} 2023-09-12T10:51:49,189 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:51:49,201 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontSize(int)’: 2023-09-12T10:51:49,201 ./src/depict/asciipainter.cpp:54:38: warning: unused parameter ‘pointSize’ [-Wunused-parameter] 2023-09-12T10:51:49,202 54 | void ASCIIPainter::SetFontSize(int pointSize) 2023-09-12T10:51:49,203 | ~~~~^~~~~~~~~ 2023-09-12T10:51:49,204 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillColor(const OpenBabel::OBColor&)’: 2023-09-12T10:51:49,204 ./src/depict/asciipainter.cpp:58:50: warning: unused parameter ‘color’ [-Wunused-parameter] 2023-09-12T10:51:49,205 58 | void ASCIIPainter::SetFillColor(const OBColor &color) 2023-09-12T10:51:49,206 | ~~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:51:49,207 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillRadial(const OpenBabel::OBColor&, const OpenBabel::OBColor&)’: 2023-09-12T10:51:49,207 ./src/depict/asciipainter.cpp:62:51: warning: unused parameter ‘start’ [-Wunused-parameter] 2023-09-12T10:51:49,208 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2023-09-12T10:51:49,209 | ~~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:51:49,209 ./src/depict/asciipainter.cpp:62:73: warning: unused parameter ‘end’ [-Wunused-parameter] 2023-09-12T10:51:49,210 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2023-09-12T10:51:49,210 | ~~~~~~~~~~~~~~~^~~ 2023-09-12T10:51:49,211 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenColor(const OpenBabel::OBColor&)’: 2023-09-12T10:51:49,212 ./src/depict/asciipainter.cpp:67:49: warning: unused parameter ‘color’ [-Wunused-parameter] 2023-09-12T10:51:49,212 67 | void ASCIIPainter::SetPenColor(const OBColor &color) 2023-09-12T10:51:49,213 | ~~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:51:49,214 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenWidth(double)’: 2023-09-12T10:51:49,214 ./src/depict/asciipainter.cpp:71:41: warning: unused parameter ‘width’ [-Wunused-parameter] 2023-09-12T10:51:49,215 71 | void ASCIIPainter::SetPenWidth(double width) 2023-09-12T10:51:49,216 | ~~~~~~~^~~~~ 2023-09-12T10:51:49,227 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawLine(double, double, double, double, const std::vector&)’: 2023-09-12T10:51:49,228 ./src/depict/asciipainter.cpp:80:103: warning: unused parameter ‘dashes’ [-Wunused-parameter] 2023-09-12T10:51:49,228 80 | void ASCIIPainter::DrawLine(double x1, double y1, double x2, double y2, const std::vector & dashes) 2023-09-12T10:51:49,229 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-09-12T10:51:49,248 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawCircle(double, double, double)’: 2023-09-12T10:51:49,248 ./src/depict/asciipainter.cpp:106:40: warning: unused parameter ‘x’ [-Wunused-parameter] 2023-09-12T10:51:49,249 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2023-09-12T10:51:49,250 | ~~~~~~~^ 2023-09-12T10:51:49,250 ./src/depict/asciipainter.cpp:106:50: warning: unused parameter ‘y’ [-Wunused-parameter] 2023-09-12T10:51:49,251 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2023-09-12T10:51:49,251 | ~~~~~~~^ 2023-09-12T10:51:49,252 ./src/depict/asciipainter.cpp:106:60: warning: unused parameter ‘r’ [-Wunused-parameter] 2023-09-12T10:51:49,253 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2023-09-12T10:51:49,254 | ~~~~~~~^ 2023-09-12T10:51:49,254 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawBall(double, double, double, double)’: 2023-09-12T10:51:49,255 ./src/depict/asciipainter.cpp:110:38: warning: unused parameter ‘x’ [-Wunused-parameter] 2023-09-12T10:51:49,256 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:51:49,257 | ~~~~~~~^ 2023-09-12T10:51:49,257 ./src/depict/asciipainter.cpp:110:48: warning: unused parameter ‘y’ [-Wunused-parameter] 2023-09-12T10:51:49,258 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:51:49,259 | ~~~~~~~^ 2023-09-12T10:51:49,260 ./src/depict/asciipainter.cpp:110:58: warning: unused parameter ‘r’ [-Wunused-parameter] 2023-09-12T10:51:49,261 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:51:49,261 | ~~~~~~~^ 2023-09-12T10:51:49,262 ./src/depict/asciipainter.cpp:110:68: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2023-09-12T10:51:49,263 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:51:49,263 | ~~~~~~~^~~~~~~ 2023-09-12T10:51:49,264 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawText(double, double, const std::string&)’: 2023-09-12T10:51:49,265 ./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] 2023-09-12T10:51:49,266 118 | for (int i=0; i search starts here: 2023-09-12T10:51:51,374 /usr/include/eigen3 2023-09-12T10:51:51,374 include 2023-09-12T10:51:51,375 /usr/include/python3.11 2023-09-12T10:51:51,375 /usr/include/c++/12 2023-09-12T10:51:51,376 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:51,377 /usr/include/c++/12/backward 2023-09-12T10:51:51,377 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:51,378 /usr/local/include 2023-09-12T10:51:51,378 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:51,379 /usr/include 2023-09-12T10:51:51,379 End of search list. 2023-09-12T10:51:51,380 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:51,381 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:51,382 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:51,382 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:51,388 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:52,634 In file included from ./src/depict/commandpainter.cpp:19: 2023-09-12T10:51:52,634 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2023-09-12T10:51:52,635 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T10:51:52,636 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2023-09-12T10:51:52,637 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:51:52,687 ./src/depict/commandpainter.cpp: In member function ‘virtual void OpenBabel::CommandPainter::DrawBall(double, double, double, double)’: 2023-09-12T10:51:52,688 ./src/depict/commandpainter.cpp:115:70: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2023-09-12T10:51:52,688 115 | void CommandPainter::DrawBall(double x, double y, double r, double opacity) 2023-09-12T10:51:52,689 | ~~~~~~~^~~~~~~ 2023-09-12T10:51:52,691 ./src/depict/commandpainter.cpp: In member function ‘virtual OpenBabel::OBFontMetrics OpenBabel::CommandPainter::GetFontMetrics(const std::string&)’: 2023-09-12T10:51:52,692 ./src/depict/commandpainter.cpp:125:67: warning: unused parameter ‘text’ [-Wunused-parameter] 2023-09-12T10:51:52,692 125 | OBFontMetrics CommandPainter::GetFontMetrics(const std::string &text) 2023-09-12T10:51:52,693 | ~~~~~~~~~~~~~~~~~~~^~~~ 2023-09-12T10:51:53,349 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:53,349 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/ccJOMvMC.s 2023-09-12T10:51:53,354 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:51:53,420 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/ 2023-09-12T10:51:53,421 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/ 2023-09-12T10:51:53,422 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/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.' 2023-09-12T10:51:53,423 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 2023-09-12T10:51:53,426 Using built-in specs. 2023-09-12T10:51:53,427 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:51:53,427 Target: arm-linux-gnueabihf 2023-09-12T10:51:53,428 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 2023-09-12T10:51:53,429 Thread model: posix 2023-09-12T10:51:53,429 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:51:53,430 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:51:53,430 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:51:53,431 /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/cc5CPoP5.s 2023-09-12T10:51:53,440 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:53,440 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:53,441 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:53,442 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:53,443 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:51:53,443 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:51:53,444 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:51:53,445 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:51:53,445 ignoring duplicate directory "/usr/include/" 2023-09-12T10:51:53,446 as it is a non-system directory that duplicates a system directory 2023-09-12T10:51:53,446 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:51:53,447 #include "..." search starts here: 2023-09-12T10:51:53,447 #include <...> search starts here: 2023-09-12T10:51:53,448 /usr/include/eigen3 2023-09-12T10:51:53,449 include 2023-09-12T10:51:53,449 /usr/include/python3.11 2023-09-12T10:51:53,450 /usr/include/c++/12 2023-09-12T10:51:53,451 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:51:53,451 /usr/include/c++/12/backward 2023-09-12T10:51:53,452 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:51:53,453 /usr/local/include 2023-09-12T10:51:53,453 /usr/include/arm-linux-gnueabihf 2023-09-12T10:51:53,454 /usr/include 2023-09-12T10:51:53,455 End of search list. 2023-09-12T10:51:53,455 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:51:53,455 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:51:53,456 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:51:53,457 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:51:53,460 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:51:55,056 In file included from include/openbabel/atom.h:33, 2023-09-12T10:51:55,057 from include/openbabel/mol.h:43, 2023-09-12T10:51:55,057 from ./src/depict/depict.cpp:20: 2023-09-12T10:51:55,058 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:51:55,058 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:51:55,059 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:51:55,060 | ^ 2023-09-12T10:51:55,060 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:51:55,061 37 | # define UNUSED(x) x 2023-09-12T10:51:55,061 | ^ 2023-09-12T10:51:55,825 In file included from include/openbabel/mol.h:52: 2023-09-12T10:51:55,826 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:55,826 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:55,827 862 | {return new OBVibrationData(*this);} 2023-09-12T10:51:55,828 | ^ 2023-09-12T10:51:55,828 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:51:55,829 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:51:55,830 | ^~~~~~~~ 2023-09-12T10:51:55,831 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:55,832 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:55,833 907 | {return new OBDOSData(*this);} 2023-09-12T10:51:55,833 | ^ 2023-09-12T10:51:55,834 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:51:55,835 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:51:55,835 | ^~~~~~~~ 2023-09-12T10:51:55,851 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:55,851 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:55,852 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:51:55,853 | ^ 2023-09-12T10:51:55,854 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:51:55,854 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:51:55,855 | ^~~~~~~~ 2023-09-12T10:51:55,858 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:51:55,858 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:51:55,859 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:51:55,859 | ^ 2023-09-12T10:51:55,860 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:51:55,860 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:51:55,861 | ^~~~~~~~ 2023-09-12T10:51:56,457 ./src/depict/depict.cpp: In function ‘unsigned int OpenBabel::GetAtomSymClass(OBAtom*)’: 2023-09-12T10:51:56,458 ./src/depict/depict.cpp:280:11: warning: unused variable ‘nclasses’ [-Wunused-variable] 2023-09-12T10:51:56,458 280 | int nclasses = end_pos - copy_sym.begin(); 2023-09-12T10:51:56,459 | ^~~~~~~~ 2023-09-12T10:51:56,647 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtom(OpenBabel::OBAtom*)’: 2023-09-12T10:51:56,647 ./src/depict/depict.cpp:839:42: warning: unused parameter ‘atom’ [-Wunused-parameter] 2023-09-12T10:51:56,648 839 | void OBDepictPrivate::DrawAtom(OBAtom *atom) 2023-09-12T10:51:56,649 | ~~~~~~~~^~~~ 2023-09-12T10:51:56,657 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtomLabel(const std::string&, int, const OpenBabel::vector3&)’: 2023-09-12T10:51:56,658 ./src/depict/depict.cpp:966:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:51:56,659 966 | OBFontMetrics metrics = painter->GetFontMetrics(str); 2023-09-12T10:51:56,659 | ^~~~~~~ 2023-09-12T10:51:56,660 ./src/depict/depict.cpp:971:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:51:56,661 971 | OBFontMetrics metrics = painter->GetFontMetrics(subscript); 2023-09-12T10:51:56,662 | ^~~~~~~ 2023-09-12T10:51:56,670 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawSimpleBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, int, bool)’: 2023-09-12T10:51:56,671 ./src/depict/depict.cpp:1011:36: warning: unused parameter ‘crossed_bond’ [-Wunused-parameter] 2023-09-12T10:51:56,672 1011 | OBAtom* endAtom, int order, bool crossed_bond) 2023-09-12T10:51:56,673 | ~~~~~^~~~~~~~~~~~ 2023-09-12T10:51:56,691 ./src/depict/depict.cpp: In member function ‘void OpenBabel::OBDepictPrivateBallAndStick::DrawAromaticRingBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, const OpenBabel::vector3&, double)’: 2023-09-12T10:51:56,692 ./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] 2023-09-12T10:51:56,692 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2023-09-12T10:51:56,693 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T10:51:56,694 ./src/depict/depict.cpp:1156:100: note: add parentheses around ‘sizeof (double)’ to silence this warning 2023-09-12T10:51:56,695 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2023-09-12T10:51:56,695 | ^~~~~~~~~~~~~~ 2023-09-12T10:51:56,696 | ( ) 2023-09-12T10:51:56,697 ./src/depict/depict.cpp:1155:24: note: array ‘dashpattern’ declared here 2023-09-12T10:51:56,697 1155 | static const float dashpattern[] = {5., 5.}; 2023-09-12T10:51:56,698 | ^~~~~~~~~~~ 2023-09-12T10:51:56,698 ./src/depict/depict.cpp:1133:152: warning: unused parameter ‘center’ [-Wunused-parameter] 2023-09-12T10:51:56,699 1133 | inline void OBDepictPrivateBallAndStick::DrawAromaticRingBond(OBAtom *prevAtom, OBAtom *beginAtom, OBAtom *endAtom, OBAtom *nextAtom, const vector3 ¢er, double dist) 2023-09-12T10:51:56,700 | ~~~~~~~~~~~~~~~^~~~~~ 2023-09-12T10:52:03,362 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:52:03,388 from include/openbabel/mol.h:35: 2023-09-12T10:52:03,436 /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 >]’: 2023-09-12T10:52:03,466 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:52:03,476 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:52:03,477 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,478 /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 >]’: 2023-09-12T10:52:03,479 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:52:03,480 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:03,482 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, 2023-09-12T10:52:03,483 inlined from ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:1052:21: 2023-09-12T10:52:03,483 /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 2023-09-12T10:52:03,484 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:03,485 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,485 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:03,486 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, 2023-09-12T10:52:03,487 inlined from ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:1053:21: 2023-09-12T10:52:03,488 /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 2023-09-12T10:52:03,488 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:03,489 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,490 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:03,490 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, 2023-09-12T10:52:03,491 inlined from ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:1055:21: 2023-09-12T10:52:03,492 /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 2023-09-12T10:52:03,492 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:03,493 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,530 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:03,530 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, 2023-09-12T10:52:03,531 inlined from ‘virtual void OpenBabel::OBDepictPrivate::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:692:21: 2023-09-12T10:52:03,532 /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 2023-09-12T10:52:03,533 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:03,534 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,535 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:03,535 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, 2023-09-12T10:52:03,536 inlined from ‘virtual void OpenBabel::OBDepictPrivate::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:693:21: 2023-09-12T10:52:03,537 /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 2023-09-12T10:52:03,538 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:03,538 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,539 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:03,540 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, 2023-09-12T10:52:03,541 inlined from ‘virtual void OpenBabel::OBDepictPrivate::DrawWedge(OpenBabel::OBAtom*, OpenBabel::OBAtom*)’ at ./src/depict/depict.cpp:695:21: 2023-09-12T10:52:03,541 /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 2023-09-12T10:52:03,542 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:03,543 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,605 In file included from /usr/include/c++/12/algorithm:61, 2023-09-12T10:52:03,606 from include/openbabel/ring.h:24, 2023-09-12T10:52:03,606 from include/openbabel/mol.h:51: 2023-09-12T10:52:03,607 /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&)>]’: 2023-09-12T10:52:03,608 /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 2023-09-12T10:52:03,608 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:52:03,609 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,610 /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 2023-09-12T10:52:03,640 /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&)>]’: 2023-09-12T10:52:03,641 /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 2023-09-12T10:52:03,642 82 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, 2023-09-12T10:52:03,643 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,644 /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 2023-09-12T10:52:03,645 /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 2023-09-12T10:52:03,646 /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 2023-09-12T10:52:03,686 In file included from /usr/include/c++/12/bits/stl_algo.h:60: 2023-09-12T10:52:03,688 /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&)>]’: 2023-09-12T10:52:03,688 /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 2023-09-12T10:52:03,689 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T10:52:03,690 | ^~~~~~~~~~~~~ 2023-09-12T10:52:03,758 /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&)>]’: 2023-09-12T10:52:03,759 /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 2023-09-12T10:52:03,759 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:52:03,760 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,761 /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 2023-09-12T10:52:03,762 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&)>]’, 2023-09-12T10:52:03,762 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: 2023-09-12T10:52:03,763 /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 2023-09-12T10:52:03,764 1887 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2023-09-12T10:52:03,765 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:03,766 1888 | __comp); 2023-09-12T10:52:03,767 | ~~~~~~~ 2023-09-12T10:52:03,768 /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 2023-09-12T10:52:03,769 /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&)>]’: 2023-09-12T10:52:03,770 /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 2023-09-12T10:52:03,771 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:52:03,771 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:04,551 ./src/depict/depict.cpp: In member function ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’: 2023-09-12T10:52:04,551 ./src/depict/depict.cpp:423:25: warning: ‘max_z’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:52:04,552 423 | d->zScale = max_z - min_z; 2023-09-12T10:52:04,553 | ~~~~~~^~~~~~~ 2023-09-12T10:52:04,553 ./src/depict/depict.cpp:395:21: note: ‘max_z’ was declared here 2023-09-12T10:52:04,554 395 | double min_z, max_z; 2023-09-12T10:52:04,555 | ^~~~~ 2023-09-12T10:52:04,556 ./src/depict/depict.cpp:423:25: warning: ‘min_z’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:52:04,556 423 | d->zScale = max_z - min_z; 2023-09-12T10:52:04,557 | ~~~~~~^~~~~~~ 2023-09-12T10:52:04,558 ./src/depict/depict.cpp:395:14: note: ‘min_z’ was declared here 2023-09-12T10:52:04,558 395 | double min_z, max_z; 2023-09-12T10:52:04,559 | ^~~~~ 2023-09-12T10:52:04,560 ./src/depict/depict.cpp:421:22: warning: ‘max_y’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:52:04,561 421 | height = max_y - min_y + 2*margin; 2023-09-12T10:52:04,562 | ~~~~~~^~~~~~~ 2023-09-12T10:52:04,563 ./src/depict/depict.cpp:394:21: note: ‘max_y’ was declared here 2023-09-12T10:52:04,565 394 | double min_y, max_y; 2023-09-12T10:52:04,566 | ^~~~~ 2023-09-12T10:52:04,567 ./src/depict/depict.cpp:421:22: warning: ‘min_y’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:52:04,567 421 | height = max_y - min_y + 2*margin; 2023-09-12T10:52:04,569 | ~~~~~~^~~~~~~ 2023-09-12T10:52:04,570 ./src/depict/depict.cpp:394:14: note: ‘min_y’ was declared here 2023-09-12T10:52:04,571 394 | double min_y, max_y; 2023-09-12T10:52:04,572 | ^~~~~ 2023-09-12T10:52:04,573 ./src/depict/depict.cpp:420:22: warning: ‘max_x’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:52:04,580 420 | width = max_x - min_x + 2*margin; 2023-09-12T10:52:04,580 | ~~~~~~^~~~~~~ 2023-09-12T10:52:04,581 ./src/depict/depict.cpp:393:21: note: ‘max_x’ was declared here 2023-09-12T10:52:04,582 393 | double min_x, max_x; 2023-09-12T10:52:04,582 | ^~~~~ 2023-09-12T10:52:04,583 ./src/depict/depict.cpp:420:22: warning: ‘min_x’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:52:04,584 420 | width = max_x - min_x + 2*margin; 2023-09-12T10:52:04,585 | ~~~~~~^~~~~~~ 2023-09-12T10:52:04,586 ./src/depict/depict.cpp:393:14: note: ‘min_x’ was declared here 2023-09-12T10:52:04,586 393 | double min_x, max_x; 2023-09-12T10:52:04,587 | ^~~~~ 2023-09-12T10:52:04,604 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:52:04,604 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:04,605 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:511:31: 2023-09-12T10:52:04,607 /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 2023-09-12T10:52:04,607 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:52:04,608 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:52:04,609 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&)>]’, 2023-09-12T10:52:04,610 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, 2023-09-12T10:52:04,611 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, 2023-09-12T10:52:04,615 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, 2023-09-12T10:52:04,616 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2023-09-12T10:52:04,617 /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 2023-09-12T10:52:04,618 1887 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2023-09-12T10:52:04,619 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:04,620 1888 | __comp); 2023-09-12T10:52:04,621 | ~~~~~~~ 2023-09-12T10:52:04,621 /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 2023-09-12T10:52:04,622 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&)>]’, 2023-09-12T10:52:04,623 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, 2023-09-12T10:52:04,681 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, 2023-09-12T10:52:04,880 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2023-09-12T10:52:04,880 /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 2023-09-12T10:52:04,881 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:52:04,883 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:04,883 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&)>]’, 2023-09-12T10:52:04,884 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, 2023-09-12T10:52:04,885 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, 2023-09-12T10:52:05,000 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2023-09-12T10:52:05,021 /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 2023-09-12T10:52:05,029 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:52:05,057 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:05,092 /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 2023-09-12T10:52:05,095 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:52:05,096 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:07,120 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:07,121 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/cc5CPoP5.s 2023-09-12T10:52:07,125 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:07,855 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/ 2023-09-12T10:52:07,856 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/ 2023-09-12T10:52:07,856 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:52:07,860 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 2023-09-12T10:52:07,864 Using built-in specs. 2023-09-12T10:52:07,864 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:07,865 Target: arm-linux-gnueabihf 2023-09-12T10:52:07,866 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 2023-09-12T10:52:07,866 Thread model: posix 2023-09-12T10:52:07,867 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:07,867 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:07,868 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:07,868 /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/ccZg5mt9.s 2023-09-12T10:52:07,877 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:07,878 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:07,879 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:07,879 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:07,880 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:07,880 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:07,881 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:07,881 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:07,882 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:07,882 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:07,883 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:07,883 #include "..." search starts here: 2023-09-12T10:52:07,884 #include <...> search starts here: 2023-09-12T10:52:07,884 /usr/include/eigen3 2023-09-12T10:52:07,884 include 2023-09-12T10:52:07,885 /usr/include/python3.11 2023-09-12T10:52:07,885 /usr/include/c++/12 2023-09-12T10:52:07,886 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:07,887 /usr/include/c++/12/backward 2023-09-12T10:52:07,887 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:07,888 /usr/local/include 2023-09-12T10:52:07,889 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:07,889 /usr/include 2023-09-12T10:52:07,890 End of search list. 2023-09-12T10:52:07,891 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:07,891 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:07,893 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:07,893 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:07,899 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:09,393 In file included from ./src/depict/svgpainter.cpp:18: 2023-09-12T10:52:09,393 include/openbabel/depict/svgpainter.h: In constructor ‘OpenBabel::SVGPainter::SVGPainter(std::ostream&, std::set >*, bool, double, double)’: 2023-09-12T10:52:09,394 include/openbabel/depict/svgpainter.h:77:11: warning: ‘OpenBabel::SVGPainter::m_fontPointSize’ will be initialized after [-Wreorder] 2023-09-12T10:52:09,395 77 | int m_fontPointSize; 2023-09-12T10:52:09,395 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:09,396 include/openbabel/depict/svgpainter.h:75:12: warning: ‘bool OpenBabel::SVGPainter::m_isFillcolor’ [-Wreorder] 2023-09-12T10:52:09,397 75 | bool m_isFillcolor; 2023-09-12T10:52:09,397 | ^~~~~~~~~~~~~ 2023-09-12T10:52:09,398 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2023-09-12T10:52:09,399 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2023-09-12T10:52:09,400 | ^~~~~~~~~~ 2023-09-12T10:52:09,400 include/openbabel/depict/svgpainter.h:75:12: warning: ‘OpenBabel::SVGPainter::m_isFillcolor’ will be initialized after [-Wreorder] 2023-09-12T10:52:09,401 75 | bool m_isFillcolor; 2023-09-12T10:52:09,402 | ^~~~~~~~~~~~~ 2023-09-12T10:52:09,403 include/openbabel/depict/svgpainter.h:74:32: warning: ‘std::set >* OpenBabel::SVGPainter::m_Gradients’ [-Wreorder] 2023-09-12T10:52:09,403 74 | std::set *m_Gradients; 2023-09-12T10:52:09,404 | ^~~~~~~~~~~ 2023-09-12T10:52:09,404 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2023-09-12T10:52:09,405 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2023-09-12T10:52:09,405 | ^~~~~~~~~~ 2023-09-12T10:52:09,495 ./src/depict/svgpainter.cpp: In member function ‘void OpenBabel::SVGPainter::WriteImage(const std::string&)’: 2023-09-12T10:52:09,496 ./src/depict/svgpainter.cpp:172:50: warning: unused parameter ‘filename’ [-Wunused-parameter] 2023-09-12T10:52:09,496 172 | void SVGPainter::WriteImage(const std::string &filename) 2023-09-12T10:52:09,497 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ 2023-09-12T10:52:11,472 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:11,473 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/ccZg5mt9.s 2023-09-12T10:52:11,477 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:11,661 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/ 2023-09-12T10:52:11,661 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/ 2023-09-12T10:52:11,662 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/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.' 2023-09-12T10:52:11,663 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 2023-09-12T10:52:11,667 Using built-in specs. 2023-09-12T10:52:11,668 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:11,668 Target: arm-linux-gnueabihf 2023-09-12T10:52:11,669 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 2023-09-12T10:52:11,670 Thread model: posix 2023-09-12T10:52:11,670 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:11,671 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:11,672 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:11,672 /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/ccjZJjy4.s 2023-09-12T10:52:11,680 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:11,681 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:11,682 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:11,683 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:11,683 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:11,684 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:11,685 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:11,685 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:11,686 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:11,686 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:11,687 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:11,688 #include "..." search starts here: 2023-09-12T10:52:11,688 #include <...> search starts here: 2023-09-12T10:52:11,689 /usr/include/eigen3 2023-09-12T10:52:11,689 include 2023-09-12T10:52:11,690 /usr/include/python3.11 2023-09-12T10:52:11,690 /usr/include/c++/12 2023-09-12T10:52:11,691 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:11,692 /usr/include/c++/12/backward 2023-09-12T10:52:11,692 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:11,693 /usr/local/include 2023-09-12T10:52:11,693 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:11,694 /usr/include 2023-09-12T10:52:11,695 End of search list. 2023-09-12T10:52:11,695 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:11,696 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 2023-09-12T10:52:11,698 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:11,698 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:11,699 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:13,362 In file included from include/openbabel/generic.h:31, 2023-09-12T10:52:13,362 from ./src/descriptor.cpp:21: 2023-09-12T10:52:13,363 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:52:13,364 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:52:13,364 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:52:13,365 | ^ 2023-09-12T10:52:13,365 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:52:13,366 37 | # define UNUSED(x) x 2023-09-12T10:52:13,366 | ^ 2023-09-12T10:52:13,567 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:13,568 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:13,568 862 | {return new OBVibrationData(*this);} 2023-09-12T10:52:13,569 | ^ 2023-09-12T10:52:13,569 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:52:13,570 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:52:13,571 | ^~~~~~~~ 2023-09-12T10:52:13,572 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:13,573 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:13,573 907 | {return new OBDOSData(*this);} 2023-09-12T10:52:13,574 | ^ 2023-09-12T10:52:13,575 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:52:13,576 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:52:13,577 | ^~~~~~~~ 2023-09-12T10:52:13,591 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:13,591 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:13,592 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:52:13,593 | ^ 2023-09-12T10:52:13,593 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:52:13,594 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:52:13,595 | ^~~~~~~~ 2023-09-12T10:52:13,597 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:13,598 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:13,599 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:52:13,599 | ^ 2023-09-12T10:52:13,600 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:52:13,600 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:52:13,601 | ^~~~~~~~ 2023-09-12T10:52:13,677 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:52:13,678 from ./src/descriptor.cpp:23: 2023-09-12T10:52:13,678 include/openbabel/plugin.h: At global scope: 2023-09-12T10:52:13,679 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:13,679 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:13,680 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:13,681 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:52:13,681 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:52:13,682 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:52:13,682 from /usr/include/c++/12/ios:42, 2023-09-12T10:52:13,683 from /usr/include/c++/12/istream:38, 2023-09-12T10:52:13,684 from /usr/include/c++/12/sstream:38, 2023-09-12T10:52:13,684 from include/openbabel/oberror.h:26, 2023-09-12T10:52:13,685 from ./src/descriptor.cpp:20: 2023-09-12T10:52:13,686 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:13,686 131 | struct binary_function 2023-09-12T10:52:13,687 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:17,609 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/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/' 2023-09-12T10:52:17,609 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/ccjZJjy4.s 2023-09-12T10:52:17,614 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:17,946 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/ 2023-09-12T10:52:17,946 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/ 2023-09-12T10:52:17,947 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:52:17,948 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 2023-09-12T10:52:17,953 Using built-in specs. 2023-09-12T10:52:17,953 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:17,954 Target: arm-linux-gnueabihf 2023-09-12T10:52:17,954 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 2023-09-12T10:52:17,955 Thread model: posix 2023-09-12T10:52:17,956 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:17,956 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:17,957 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:17,957 /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/ccU3LPB4.s 2023-09-12T10:52:17,966 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:17,967 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 2023-09-12T10:52:17,968 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:17,969 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:17,969 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:17,970 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:17,971 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:17,972 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:17,972 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:17,972 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:17,973 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:17,973 #include "..." search starts here: 2023-09-12T10:52:17,974 #include <...> search starts here: 2023-09-12T10:52:17,974 /usr/include/eigen3 2023-09-12T10:52:17,975 include 2023-09-12T10:52:17,975 /usr/include/python3.11 2023-09-12T10:52:17,975 /usr/include/c++/12 2023-09-12T10:52:17,976 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:17,976 /usr/include/c++/12/backward 2023-09-12T10:52:17,977 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:17,977 /usr/local/include 2023-09-12T10:52:17,978 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:17,978 /usr/include 2023-09-12T10:52:17,979 End of search list. 2023-09-12T10:52:17,979 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:17,980 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:17,981 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:17,981 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:17,984 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:19,648 In file included from include/openbabel/format.h:22, 2023-09-12T10:52:19,682 from include/openbabel/obconversion.h:37, 2023-09-12T10:52:19,685 from ./src/descriptors/cansmidescriptor.cpp:22: 2023-09-12T10:52:19,776 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:19,813 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:19,814 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:19,815 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:52:19,816 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:52:19,817 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:52:19,817 from /usr/include/c++/12/ios:42, 2023-09-12T10:52:19,818 from /usr/include/c++/12/istream:38, 2023-09-12T10:52:19,819 from /usr/include/c++/12/sstream:38, 2023-09-12T10:52:19,820 from include/openbabel/oberror.h:26, 2023-09-12T10:52:19,820 from ./src/descriptors/cansmidescriptor.cpp:20: 2023-09-12T10:52:19,821 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:19,822 131 | struct binary_function 2023-09-12T10:52:19,823 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:19,925 ./src/descriptors/cansmidescriptor.cpp: In member function ‘virtual bool OpenBabel::CanSmiles::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2023-09-12T10:52:19,926 ./src/descriptors/cansmidescriptor.cpp:42:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:52:19,927 42 | bool CanSmiles::Compare(OBBase* pOb, istream& optionText, bool noEval, string* param) 2023-09-12T10:52:19,935 | ~~~~~~~~^~~~~ 2023-09-12T10:52:21,120 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:21,121 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/ccU3LPB4.s 2023-09-12T10:52:21,125 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:21,226 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/ 2023-09-12T10:52:21,227 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/ 2023-09-12T10:52:21,229 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:52:21,229 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 2023-09-12T10:52:21,232 Using built-in specs. 2023-09-12T10:52:21,233 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:21,234 Target: arm-linux-gnueabihf 2023-09-12T10:52:21,234 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 2023-09-12T10:52:21,235 Thread model: posix 2023-09-12T10:52:21,235 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:21,236 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:21,236 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/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/' 2023-09-12T10:52:21,237 /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/ccEgRAXl.s 2023-09-12T10:52:21,246 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:21,246 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 2023-09-12T10:52:21,247 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:21,248 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:21,248 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:21,249 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:21,249 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:21,250 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:21,250 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:21,251 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:21,251 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:21,252 #include "..." search starts here: 2023-09-12T10:52:21,252 #include <...> search starts here: 2023-09-12T10:52:21,253 /usr/include/eigen3 2023-09-12T10:52:21,253 include 2023-09-12T10:52:21,254 /usr/include/python3.11 2023-09-12T10:52:21,255 /usr/include/c++/12 2023-09-12T10:52:21,255 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:21,256 /usr/include/c++/12/backward 2023-09-12T10:52:21,257 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:21,257 /usr/local/include 2023-09-12T10:52:21,258 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:21,258 /usr/include 2023-09-12T10:52:21,259 End of search list. 2023-09-12T10:52:21,260 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:21,260 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:21,262 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:21,262 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:21,265 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:22,641 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:52:22,642 from ./src/descriptors/cmpdfilter.cpp:21: 2023-09-12T10:52:22,642 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:22,643 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:22,644 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:22,644 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:52:22,645 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:52:22,646 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:52:22,647 from /usr/include/c++/12/ios:42, 2023-09-12T10:52:22,647 from /usr/include/c++/12/istream:38, 2023-09-12T10:52:22,648 from /usr/include/c++/12/sstream:38, 2023-09-12T10:52:22,649 from include/openbabel/oberror.h:26, 2023-09-12T10:52:22,649 from ./src/descriptors/cmpdfilter.cpp:20: 2023-09-12T10:52:22,650 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:22,650 131 | struct binary_function 2023-09-12T10:52:22,651 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:22,706 ./src/descriptors/cmpdfilter.cpp: In member function ‘virtual bool OpenBabel::CompoundFilter::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2023-09-12T10:52:22,707 ./src/descriptors/cmpdfilter.cpp:74:68: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:52:22,707 74 | virtual bool Compare(OBBase* pOb, istream&, bool noEval, string* param) 2023-09-12T10:52:22,708 | ~~~~~~~~^~~~~ 2023-09-12T10:52:23,990 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/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/' 2023-09-12T10:52:23,991 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/ccEgRAXl.s 2023-09-12T10:52:23,995 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:24,098 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/ 2023-09-12T10:52:24,098 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/ 2023-09-12T10:52:24,099 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/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.' 2023-09-12T10:52:24,099 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 2023-09-12T10:52:24,103 Using built-in specs. 2023-09-12T10:52:24,104 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:24,105 Target: arm-linux-gnueabihf 2023-09-12T10:52:24,105 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 2023-09-12T10:52:24,106 Thread model: posix 2023-09-12T10:52:24,107 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:24,107 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:24,108 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/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/' 2023-09-12T10:52:24,108 /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/ccQU0VLX.s 2023-09-12T10:52:24,117 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:24,117 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:24,119 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:24,119 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:24,120 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:24,120 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:24,121 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:24,122 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:24,122 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:24,123 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:24,123 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:24,124 #include "..." search starts here: 2023-09-12T10:52:24,124 #include <...> search starts here: 2023-09-12T10:52:24,125 /usr/include/eigen3 2023-09-12T10:52:24,125 include 2023-09-12T10:52:24,126 /usr/include/python3.11 2023-09-12T10:52:24,127 /usr/include/c++/12 2023-09-12T10:52:24,127 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:24,128 /usr/include/c++/12/backward 2023-09-12T10:52:24,129 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:24,129 /usr/local/include 2023-09-12T10:52:24,130 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:24,131 /usr/include 2023-09-12T10:52:24,131 End of search list. 2023-09-12T10:52:24,132 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:24,133 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:24,134 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:24,134 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:24,135 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:25,798 In file included from include/openbabel/atom.h:33, 2023-09-12T10:52:25,799 from include/openbabel/mol.h:43, 2023-09-12T10:52:25,799 from ./src/descriptors/filters.cpp:21: 2023-09-12T10:52:25,800 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:52:25,800 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:52:25,801 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:52:25,801 | ^ 2023-09-12T10:52:25,802 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:52:25,803 37 | # define UNUSED(x) x 2023-09-12T10:52:25,803 | ^ 2023-09-12T10:52:26,486 In file included from include/openbabel/mol.h:52: 2023-09-12T10:52:26,486 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:26,487 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:26,488 862 | {return new OBVibrationData(*this);} 2023-09-12T10:52:26,488 | ^ 2023-09-12T10:52:26,489 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:52:26,490 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:52:26,490 | ^~~~~~~~ 2023-09-12T10:52:26,491 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:26,492 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:26,493 907 | {return new OBDOSData(*this);} 2023-09-12T10:52:26,494 | ^ 2023-09-12T10:52:26,495 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:52:26,495 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:52:26,496 | ^~~~~~~~ 2023-09-12T10:52:26,510 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:26,511 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:26,512 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:52:26,512 | ^ 2023-09-12T10:52:26,513 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:52:26,514 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:52:26,515 | ^~~~~~~~ 2023-09-12T10:52:26,517 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:26,518 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:26,518 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:52:26,519 | ^ 2023-09-12T10:52:26,520 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:52:26,520 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:52:26,521 | ^~~~~~~~ 2023-09-12T10:52:26,692 In file included from include/openbabel/format.h:22, 2023-09-12T10:52:26,692 from include/openbabel/obconversion.h:37, 2023-09-12T10:52:26,693 from ./src/descriptors/filters.cpp:22: 2023-09-12T10:52:26,694 include/openbabel/plugin.h: At global scope: 2023-09-12T10:52:26,694 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:26,695 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:26,695 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:26,696 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:52:26,697 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:52:26,697 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:52:26,698 from /usr/include/c++/12/ios:42, 2023-09-12T10:52:26,699 from /usr/include/c++/12/istream:38, 2023-09-12T10:52:26,700 from /usr/include/c++/12/sstream:38, 2023-09-12T10:52:26,700 from include/openbabel/oberror.h:26, 2023-09-12T10:52:26,701 from ./src/descriptors/filters.cpp:20: 2023-09-12T10:52:26,702 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:26,702 131 | struct binary_function 2023-09-12T10:52:26,703 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:26,892 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::MWFilter::Predict(OpenBabel::OBBase*, std::string*)’: 2023-09-12T10:52:26,892 ./src/descriptors/filters.cpp:36:47: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:52:26,893 36 | virtual double Predict(OBBase* pOb, string* param=NULL) 2023-09-12T10:52:26,894 | ^ 2023-09-12T10:52:26,902 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::FormulaDescriptor::GetStringValue(OpenBabel::OBBase*, std::string&, std::string*)’: 2023-09-12T10:52:26,903 ./src/descriptors/filters.cpp:142:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:52:26,903 142 | virtual double GetStringValue(OBBase* pOb, std::string& svalue, std::string* param=NULL) 2023-09-12T10:52:26,904 | ^ 2023-09-12T10:52:29,283 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:29,284 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/ccQU0VLX.s 2023-09-12T10:52:29,288 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:29,422 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/ 2023-09-12T10:52:29,423 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/ 2023-09-12T10:52:29,423 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:52:29,424 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 2023-09-12T10:52:29,429 Using built-in specs. 2023-09-12T10:52:29,429 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:29,430 Target: arm-linux-gnueabihf 2023-09-12T10:52:29,430 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 2023-09-12T10:52:29,431 Thread model: posix 2023-09-12T10:52:29,432 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:29,432 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:29,433 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:29,433 /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/ccL2dfge.s 2023-09-12T10:52:29,442 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:29,443 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:29,444 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:29,444 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:29,445 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:29,445 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:29,446 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:29,446 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:29,447 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:29,447 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:29,448 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:29,448 #include "..." search starts here: 2023-09-12T10:52:29,449 #include <...> search starts here: 2023-09-12T10:52:29,450 /usr/include/eigen3 2023-09-12T10:52:29,450 include 2023-09-12T10:52:29,451 /usr/include/python3.11 2023-09-12T10:52:29,452 /usr/include/c++/12 2023-09-12T10:52:29,452 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:29,453 /usr/include/c++/12/backward 2023-09-12T10:52:29,453 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:29,454 /usr/local/include 2023-09-12T10:52:29,455 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:29,455 /usr/include 2023-09-12T10:52:29,456 End of search list. 2023-09-12T10:52:29,457 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:29,457 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 2023-09-12T10:52:29,459 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:29,459 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:29,462 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:31,040 In file included from include/openbabel/atom.h:33, 2023-09-12T10:52:31,041 from include/openbabel/mol.h:43, 2023-09-12T10:52:31,042 from ./src/descriptors/groupcontrib.cpp:27: 2023-09-12T10:52:31,042 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:52:31,043 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:52:31,044 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:52:31,044 | ^ 2023-09-12T10:52:31,045 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:52:31,046 37 | # define UNUSED(x) x 2023-09-12T10:52:31,046 | ^ 2023-09-12T10:52:31,809 In file included from include/openbabel/mol.h:52: 2023-09-12T10:52:31,810 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:31,811 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:31,811 862 | {return new OBVibrationData(*this);} 2023-09-12T10:52:31,812 | ^ 2023-09-12T10:52:31,813 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:52:31,813 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:52:31,814 | ^~~~~~~~ 2023-09-12T10:52:31,815 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:31,815 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:31,816 907 | {return new OBDOSData(*this);} 2023-09-12T10:52:31,817 | ^ 2023-09-12T10:52:31,817 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:52:31,818 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:52:31,819 | ^~~~~~~~ 2023-09-12T10:52:31,834 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:31,835 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:31,835 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:52:31,836 | ^ 2023-09-12T10:52:31,837 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:52:31,838 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:52:31,839 | ^~~~~~~~ 2023-09-12T10:52:31,841 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:31,842 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:31,843 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:52:31,843 | ^ 2023-09-12T10:52:31,844 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:52:31,845 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:52:31,846 | ^~~~~~~~ 2023-09-12T10:52:32,053 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:52:32,054 from include/openbabel/groupcontrib.h:28, 2023-09-12T10:52:32,055 from ./src/descriptors/groupcontrib.cpp:29: 2023-09-12T10:52:32,056 include/openbabel/plugin.h: At global scope: 2023-09-12T10:52:32,056 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:32,057 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:32,058 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:32,059 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:52:32,059 from /usr/include/c++/12/vector:66, 2023-09-12T10:52:32,060 from ./src/descriptors/groupcontrib.cpp:25: 2023-09-12T10:52:32,060 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:32,061 131 | struct binary_function 2023-09-12T10:52:32,061 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:32,306 ./src/descriptors/groupcontrib.cpp: In member function ‘virtual double OpenBabel::OBGroupContrib::Predict(OpenBabel::OBBase*, std::string*)’: 2023-09-12T10:52:32,307 ./src/descriptors/groupcontrib.cpp:106:55: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:52:32,308 106 | double OBGroupContrib::Predict(OBBase* pOb, string* param) 2023-09-12T10:52:32,308 | ~~~~~~~~^~~~~ 2023-09-12T10:52:35,015 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:52:35,015 /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 >]’: 2023-09-12T10:52:35,016 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2023-09-12T10:52:35,017 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:52:35,017 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:35,160 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:35,160 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, 2023-09-12T10:52:35,161 inlined from ‘bool OpenBabel::OBGroupContrib::ParseFile()’ at ./src/descriptors/groupcontrib.cpp:83:35: 2023-09-12T10:52:35,162 /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 2023-09-12T10:52:35,163 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:35,163 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:35,164 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2023-09-12T10:52:35,165 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, 2023-09-12T10:52:35,165 inlined from ‘bool OpenBabel::OBGroupContrib::ParseFile()’ at ./src/descriptors/groupcontrib.cpp:85:38: 2023-09-12T10:52:35,166 /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 2023-09-12T10:52:35,167 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:52:35,167 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:52:36,549 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:36,549 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/ccL2dfge.s 2023-09-12T10:52:36,554 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:36,856 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/ 2023-09-12T10:52:36,857 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/ 2023-09-12T10:52:36,857 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:52:36,859 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 2023-09-12T10:52:36,863 Using built-in specs. 2023-09-12T10:52:36,864 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:36,864 Target: arm-linux-gnueabihf 2023-09-12T10:52:36,865 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 2023-09-12T10:52:36,866 Thread model: posix 2023-09-12T10:52:36,866 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:36,867 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:36,867 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:36,868 /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/ccdYDYbA.s 2023-09-12T10:52:36,876 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:36,877 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:36,878 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:36,879 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:36,879 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:36,880 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:36,881 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:36,881 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:36,882 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:36,883 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:36,883 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:36,884 #include "..." search starts here: 2023-09-12T10:52:36,885 #include <...> search starts here: 2023-09-12T10:52:36,885 /usr/include/eigen3 2023-09-12T10:52:36,886 include 2023-09-12T10:52:36,886 /usr/include/python3.11 2023-09-12T10:52:36,887 /usr/include/c++/12 2023-09-12T10:52:36,887 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:36,888 /usr/include/c++/12/backward 2023-09-12T10:52:36,888 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:36,889 /usr/local/include 2023-09-12T10:52:36,890 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:36,890 /usr/include 2023-09-12T10:52:36,891 End of search list. 2023-09-12T10:52:36,891 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:36,892 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:36,893 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:36,894 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:36,900 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:38,534 In file included from include/openbabel/atom.h:33, 2023-09-12T10:52:38,535 from include/openbabel/mol.h:43, 2023-09-12T10:52:38,535 from ./src/descriptors/smartsdescriptors.cpp:21: 2023-09-12T10:52:38,536 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:52:38,537 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:52:38,537 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:52:38,538 | ^ 2023-09-12T10:52:38,538 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:52:38,539 37 | # define UNUSED(x) x 2023-09-12T10:52:38,539 | ^ 2023-09-12T10:52:39,222 In file included from include/openbabel/mol.h:52: 2023-09-12T10:52:39,223 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:39,223 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:39,224 862 | {return new OBVibrationData(*this);} 2023-09-12T10:52:39,225 | ^ 2023-09-12T10:52:39,225 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:52:39,226 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:52:39,227 | ^~~~~~~~ 2023-09-12T10:52:39,229 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:39,229 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:39,230 907 | {return new OBDOSData(*this);} 2023-09-12T10:52:39,231 | ^ 2023-09-12T10:52:39,232 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:52:39,232 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:52:39,233 | ^~~~~~~~ 2023-09-12T10:52:39,248 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:39,249 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:39,250 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:52:39,251 | ^ 2023-09-12T10:52:39,251 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:52:39,252 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:52:39,253 | ^~~~~~~~ 2023-09-12T10:52:39,255 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:39,256 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:39,257 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:52:39,258 | ^ 2023-09-12T10:52:39,259 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:52:39,259 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:52:39,260 | ^~~~~~~~ 2023-09-12T10:52:39,478 In file included from include/openbabel/descriptor.h:27, 2023-09-12T10:52:39,478 from ./src/descriptors/smartsdescriptors.cpp:22: 2023-09-12T10:52:39,479 include/openbabel/plugin.h: At global scope: 2023-09-12T10:52:39,480 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:39,480 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:39,481 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:39,481 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:52:39,482 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:52:39,482 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:52:39,483 from /usr/include/c++/12/ios:42, 2023-09-12T10:52:39,484 from /usr/include/c++/12/istream:38, 2023-09-12T10:52:39,484 from /usr/include/c++/12/sstream:38, 2023-09-12T10:52:39,485 from include/openbabel/oberror.h:26, 2023-09-12T10:52:39,485 from ./src/descriptors/smartsdescriptors.cpp:20: 2023-09-12T10:52:39,486 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:39,487 131 | struct binary_function 2023-09-12T10:52:39,487 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:39,530 ./src/descriptors/smartsdescriptors.cpp: In member function ‘virtual double OpenBabel::SmartsDescriptor::Predict(OpenBabel::OBBase*, std::string*)’: 2023-09-12T10:52:39,530 ./src/descriptors/smartsdescriptors.cpp:48:41: warning: unused parameter ‘param’ [-Wunused-parameter] 2023-09-12T10:52:39,531 48 | double Predict(OBBase* pOb, string* param=NULL) 2023-09-12T10:52:39,532 | ^ 2023-09-12T10:52:41,646 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:41,646 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/descriptors/smartsdescriptors.o /tmp/ccdYDYbA.s 2023-09-12T10:52:41,651 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:41,757 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/ 2023-09-12T10:52:41,757 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/ 2023-09-12T10:52:41,758 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:52:41,759 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 2023-09-12T10:52:41,763 Using built-in specs. 2023-09-12T10:52:41,764 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:41,764 Target: arm-linux-gnueabihf 2023-09-12T10:52:41,765 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 2023-09-12T10:52:41,765 Thread model: posix 2023-09-12T10:52:41,766 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:41,766 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:41,767 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:41,767 /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/cc1TSr1g.s 2023-09-12T10:52:41,776 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:41,777 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:41,778 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:41,779 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:41,780 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:41,780 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:41,781 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:41,782 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:41,782 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:41,783 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:41,783 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:41,784 #include "..." search starts here: 2023-09-12T10:52:41,784 #include <...> search starts here: 2023-09-12T10:52:41,785 /usr/include/eigen3 2023-09-12T10:52:41,785 include 2023-09-12T10:52:41,786 /usr/include/python3.11 2023-09-12T10:52:41,786 /usr/include/c++/12 2023-09-12T10:52:41,787 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:41,787 /usr/include/c++/12/backward 2023-09-12T10:52:41,788 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:41,788 /usr/local/include 2023-09-12T10:52:41,788 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:41,789 /usr/include 2023-09-12T10:52:41,790 End of search list. 2023-09-12T10:52:41,790 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:41,791 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:41,791 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:41,792 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:41,794 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:42,320 ./src/distgeom.cpp:37: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2023-09-12T10:52:42,321 37 | #pragma warning(disable : 4244) // warning C4244: '=' : conversion from 'double' to 'float', possible loss of data 2023-09-12T10:52:42,322 | 2023-09-12T10:52:42,322 ./src/distgeom.cpp:38: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2023-09-12T10:52:42,323 38 | #pragma warning(disable : 4305) // warning C4305: '*=' : truncation from 'double' to 'float' 2023-09-12T10:52:42,323 | 2023-09-12T10:52:42,324 ./src/distgeom.cpp:524:3: warning: multi-line comment [-Wcomment] 2023-09-12T10:52:42,324 524 | // \ 2023-09-12T10:52:42,325 | ^ 2023-09-12T10:52:42,326 ./src/distgeom.cpp:881:9: warning: multi-line comment [-Wcomment] 2023-09-12T10:52:42,327 881 | // / \ 2023-09-12T10:52:42,327 | ^ 2023-09-12T10:52:43,556 In file included from include/openbabel/atom.h:33, 2023-09-12T10:52:43,557 from include/openbabel/mol.h:43, 2023-09-12T10:52:43,557 from include/openbabel/distgeom.h:24, 2023-09-12T10:52:43,558 from ./src/distgeom.cpp:20: 2023-09-12T10:52:43,559 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:52:43,559 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:52:43,560 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:52:43,561 | ^ 2023-09-12T10:52:43,561 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:52:43,562 37 | # define UNUSED(x) x 2023-09-12T10:52:43,563 | ^ 2023-09-12T10:52:44,322 In file included from include/openbabel/mol.h:52: 2023-09-12T10:52:44,323 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:44,324 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:44,325 862 | {return new OBVibrationData(*this);} 2023-09-12T10:52:44,326 | ^ 2023-09-12T10:52:44,326 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:52:44,327 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:52:44,328 | ^~~~~~~~ 2023-09-12T10:52:44,328 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:44,329 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:44,329 907 | {return new OBDOSData(*this);} 2023-09-12T10:52:44,330 | ^ 2023-09-12T10:52:44,330 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:52:44,331 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:52:44,332 | ^~~~~~~~ 2023-09-12T10:52:44,346 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:44,347 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:44,348 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:52:44,349 | ^ 2023-09-12T10:52:44,349 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:52:44,350 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:52:44,351 | ^~~~~~~~ 2023-09-12T10:52:44,353 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:52:44,354 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:52:44,354 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:52:44,355 | ^ 2023-09-12T10:52:44,356 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:52:44,357 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:52:44,358 | ^~~~~~~~ 2023-09-12T10:52:46,240 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set14Bounds()’: 2023-09-12T10:52:46,241 ./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] 2023-09-12T10:52:46,242 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:52:46,242 ./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] 2023-09-12T10:52:46,243 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:52:46,244 ./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] 2023-09-12T10:52:46,245 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:52:46,245 ./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] 2023-09-12T10:52:46,246 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:52:46,246 ./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] 2023-09-12T10:52:46,247 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:52:46,247 ./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] 2023-09-12T10:52:46,248 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2023-09-12T10:52:46,249 ./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] 2023-09-12T10:52:46,249 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:52:46,250 ./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] 2023-09-12T10:52:46,250 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2023-09-12T10:52:46,251 ./src/distgeom.cpp:386:18: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-12T10:52:46,252 386 | unsigned int i, j; 2023-09-12T10:52:46,253 | ^ 2023-09-12T10:52:46,253 ./src/distgeom.cpp:386:21: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-12T10:52:46,254 386 | unsigned int i, j; 2023-09-12T10:52:46,255 | ^ 2023-09-12T10:52:46,256 ./src/distgeom.cpp:426:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2023-09-12T10:52:46,256 426 | OBStereo::Ref bond_id; 2023-09-12T10:52:46,257 | ^~~~~~~ 2023-09-12T10:52:46,258 ./src/distgeom.cpp: In member function ‘OpenBabel::OBCisTransStereo* OpenBabel::OBDistanceGeometry::GetCisTransStereo(OpenBabel::OBBond*)’: 2023-09-12T10:52:46,258 ./src/distgeom.cpp:584:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2023-09-12T10:52:46,259 584 | OBStereo::Ref bond_id; 2023-09-12T10:52:46,260 | ^~~~~~~ 2023-09-12T10:52:46,264 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set15Bounds()’: 2023-09-12T10:52:46,265 ./src/distgeom.cpp:614:18: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-12T10:52:46,266 614 | unsigned int i, j; 2023-09-12T10:52:46,267 | ^ 2023-09-12T10:52:46,267 ./src/distgeom.cpp:614:21: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-12T10:52:46,268 614 | unsigned int i, j; 2023-09-12T10:52:46,269 | ^ 2023-09-12T10:52:46,274 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::TriangleSmooth(int)’: 2023-09-12T10:52:46,275 ./src/distgeom.cpp:745:9: warning: unused variable ‘loopCount’ [-Wunused-variable] 2023-09-12T10:52:46,276 745 | int loopCount = 0; 2023-09-12T10:52:46,277 | ^~~~~~~~~ 2023-09-12T10:52:46,277 ./src/distgeom.cpp:742:47: warning: unused parameter ‘iterations’ [-Wunused-parameter] 2023-09-12T10:52:46,278 742 | void OBDistanceGeometry::TriangleSmooth(int iterations) 2023-09-12T10:52:46,278 | ~~~~^~~~~~~~~~ 2023-09-12T10:52:46,346 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::AddConformer()’: 2023-09-12T10:52:46,347 ./src/distgeom.cpp:1105:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:52:46,348 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2023-09-12T10:52:46,348 | ~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T10:52:46,349 ./src/distgeom.cpp:1105:52: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:52:46,349 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2023-09-12T10:52:46,350 | ~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T10:52:46,351 ./src/distgeom.cpp:1105:77: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:52:46,351 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2023-09-12T10:52:46,352 | ~~~~~~~~~~~~^~~~~~~~ 2023-09-12T10:52:46,353 ./src/distgeom.cpp:1039:18: warning: unused variable ‘attempts’ [-Wunused-variable] 2023-09-12T10:52:46,354 1039 | unsigned int attempts = 0; 2023-09-12T10:52:46,355 | ^~~~~~~~ 2023-09-12T10:52:56,974 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:56,975 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/cc1TSr1g.s 2023-09-12T10:52:56,983 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:57,942 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/ 2023-09-12T10:52:57,943 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/ 2023-09-12T10:52:57,943 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/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.' 2023-09-12T10:52:57,947 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 2023-09-12T10:52:57,952 Using built-in specs. 2023-09-12T10:52:57,953 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:57,953 Target: arm-linux-gnueabihf 2023-09-12T10:52:57,954 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 2023-09-12T10:52:57,954 Thread model: posix 2023-09-12T10:52:57,954 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:57,955 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:57,955 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:57,956 /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/ccGHtBBh.s 2023-09-12T10:52:57,965 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:57,966 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:57,967 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:57,968 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:57,968 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:57,969 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:57,969 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:57,970 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:57,971 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:57,971 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:57,972 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:57,973 #include "..." search starts here: 2023-09-12T10:52:57,973 #include <...> search starts here: 2023-09-12T10:52:57,974 /usr/include/eigen3 2023-09-12T10:52:57,974 include 2023-09-12T10:52:57,974 /usr/include/python3.11 2023-09-12T10:52:57,975 /usr/include/c++/12 2023-09-12T10:52:57,975 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:57,976 /usr/include/c++/12/backward 2023-09-12T10:52:57,976 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:57,976 /usr/local/include 2023-09-12T10:52:57,977 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:57,977 /usr/include 2023-09-12T10:52:57,978 End of search list. 2023-09-12T10:52:57,978 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:57,979 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:57,980 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:57,980 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:57,986 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:58,005 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:58,005 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/ccGHtBBh.s 2023-09-12T10:52:58,010 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:52:58,014 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/ 2023-09-12T10:52:58,016 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/ 2023-09-12T10:52:58,016 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/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.' 2023-09-12T10:52:58,017 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 2023-09-12T10:52:58,020 Using built-in specs. 2023-09-12T10:52:58,021 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:52:58,021 Target: arm-linux-gnueabihf 2023-09-12T10:52:58,022 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 2023-09-12T10:52:58,022 Thread model: posix 2023-09-12T10:52:58,023 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:52:58,024 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:52:58,024 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:52:58,025 /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/cc4KvNg3.s 2023-09-12T10:52:58,033 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:58,034 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:58,035 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:58,036 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:58,037 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:52:58,037 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:52:58,038 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:52:58,038 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:52:58,039 ignoring duplicate directory "/usr/include/" 2023-09-12T10:52:58,040 as it is a non-system directory that duplicates a system directory 2023-09-12T10:52:58,040 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:52:58,041 #include "..." search starts here: 2023-09-12T10:52:58,041 #include <...> search starts here: 2023-09-12T10:52:58,042 /usr/include/eigen3 2023-09-12T10:52:58,042 include 2023-09-12T10:52:58,043 /usr/include/python3.11 2023-09-12T10:52:58,044 /usr/include/c++/12 2023-09-12T10:52:58,044 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:52:58,045 /usr/include/c++/12/backward 2023-09-12T10:52:58,046 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:52:58,046 /usr/local/include 2023-09-12T10:52:58,047 /usr/include/arm-linux-gnueabihf 2023-09-12T10:52:58,048 /usr/include 2023-09-12T10:52:58,049 End of search list. 2023-09-12T10:52:58,049 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:52:58,050 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:52:58,051 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:52:58,051 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:52:58,055 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:52:59,564 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:52:59,565 from ./src/fingerprint.cpp:27: 2023-09-12T10:52:59,565 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:52:59,566 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:52:59,566 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:59,567 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:52:59,567 from /usr/include/c++/12/vector:66, 2023-09-12T10:52:59,568 from ./src/fingerprint.cpp:21: 2023-09-12T10:52:59,568 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:52:59,569 131 | struct binary_function 2023-09-12T10:52:59,569 | ^~~~~~~~~~~~~~~ 2023-09-12T10:52:59,719 ./src/fingerprint.cpp: In member function ‘bool OpenBabel::FastSearch::Find(OpenBabel::OBBase*, std::vector&, unsigned int)’: 2023-09-12T10:52:59,720 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2023-09-12T10:52:59,720 161 | if ( (a=((*ppat) & (*p++)) ^ (*ppat++)) ) break; 2023-09-12T10:52:59,721 | ~~~~^~ 2023-09-12T10:52:59,722 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2023-09-12T10:53:02,486 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/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/' 2023-09-12T10:53:02,486 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/fingerprint.o /tmp/cc4KvNg3.s 2023-09-12T10:53:02,491 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:03,187 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/ 2023-09-12T10:53:03,188 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/ 2023-09-12T10:53:03,189 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:53:03,192 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 2023-09-12T10:53:03,201 Using built-in specs. 2023-09-12T10:53:03,203 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:03,204 Target: arm-linux-gnueabihf 2023-09-12T10:53:03,205 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 2023-09-12T10:53:03,205 Thread model: posix 2023-09-12T10:53:03,206 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:03,207 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:03,208 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:53:03,209 /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/ccFgQ6oB.s 2023-09-12T10:53:03,228 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:03,229 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:03,231 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:03,232 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:03,233 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:03,234 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:03,235 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:03,236 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:03,237 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:03,238 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:03,238 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:03,239 #include "..." search starts here: 2023-09-12T10:53:03,240 #include <...> search starts here: 2023-09-12T10:53:03,240 /usr/include/eigen3 2023-09-12T10:53:03,241 include 2023-09-12T10:53:03,241 /usr/include/python3.11 2023-09-12T10:53:03,242 /usr/include/c++/12 2023-09-12T10:53:03,243 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:03,243 /usr/include/c++/12/backward 2023-09-12T10:53:03,244 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:03,245 /usr/local/include 2023-09-12T10:53:03,245 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:03,246 /usr/include 2023-09-12T10:53:03,246 End of search list. 2023-09-12T10:53:03,247 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:03,248 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:03,249 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:03,250 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:03,260 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:08,485 In file included from include/openbabel/atom.h:33, 2023-09-12T10:53:08,500 from include/openbabel/mol.h:43, 2023-09-12T10:53:08,501 from ./src/fingerprints/finger2.cpp:20: 2023-09-12T10:53:08,595 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:08,692 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:08,743 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:08,867 | ^ 2023-09-12T10:53:08,874 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:08,880 37 | # define UNUSED(x) x 2023-09-12T10:53:08,880 | ^ 2023-09-12T10:53:09,684 In file included from include/openbabel/mol.h:52: 2023-09-12T10:53:09,684 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:09,685 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:09,686 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:09,687 | ^ 2023-09-12T10:53:09,688 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:09,689 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:09,690 | ^~~~~~~~ 2023-09-12T10:53:09,692 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:09,693 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:09,694 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:09,695 | ^ 2023-09-12T10:53:09,696 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:09,696 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:09,698 | ^~~~~~~~ 2023-09-12T10:53:09,714 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:09,714 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:09,715 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:09,715 | ^ 2023-09-12T10:53:09,716 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:09,717 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:09,717 | ^~~~~~~~ 2023-09-12T10:53:09,722 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:09,723 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:09,723 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:09,724 | ^ 2023-09-12T10:53:09,725 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:09,725 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:09,726 | ^~~~~~~~ 2023-09-12T10:53:09,916 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:53:09,917 from ./src/fingerprints/finger2.cpp:21: 2023-09-12T10:53:09,917 include/openbabel/plugin.h: At global scope: 2023-09-12T10:53:09,918 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:53:09,919 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:53:09,920 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:09,921 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:53:09,921 from /usr/include/c++/12/vector:66, 2023-09-12T10:53:09,922 from include/openbabel/mol.h:35: 2023-09-12T10:53:09,922 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:53:09,923 131 | struct binary_function 2023-09-12T10:53:09,924 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:09,994 ./src/fingerprints/finger2.cpp: In member function ‘virtual std::string OpenBabel::fingerprint2::DescribeBits(std::vector, bool)’: 2023-09-12T10:53:09,994 ./src/fingerprints/finger2.cpp:63:68: warning: unused parameter ‘fp’ [-Wunused-parameter] 2023-09-12T10:53:09,995 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:53:09,996 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2023-09-12T10:53:09,997 ./src/fingerprints/finger2.cpp:63:77: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2023-09-12T10:53:09,998 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:53:09,998 | ~~~~~^~~~~~~~~ 2023-09-12T10:53:14,513 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:53:14,514 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/ccFgQ6oB.s 2023-09-12T10:53:14,518 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:14,840 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/ 2023-09-12T10:53:14,840 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/ 2023-09-12T10:53:14,841 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/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.' 2023-09-12T10:53:14,843 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 2023-09-12T10:53:14,847 Using built-in specs. 2023-09-12T10:53:14,848 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:14,848 Target: arm-linux-gnueabihf 2023-09-12T10:53:14,849 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 2023-09-12T10:53:14,850 Thread model: posix 2023-09-12T10:53:14,850 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:14,851 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:14,851 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:53:14,852 /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/ccu3V50I.s 2023-09-12T10:53:14,861 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:14,861 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:14,862 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:14,863 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:14,863 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:14,864 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:14,864 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:14,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:14,866 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:14,866 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:14,867 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:14,868 #include "..." search starts here: 2023-09-12T10:53:14,868 #include <...> search starts here: 2023-09-12T10:53:14,869 /usr/include/eigen3 2023-09-12T10:53:14,870 include 2023-09-12T10:53:14,870 /usr/include/python3.11 2023-09-12T10:53:14,871 /usr/include/c++/12 2023-09-12T10:53:14,872 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:14,872 /usr/include/c++/12/backward 2023-09-12T10:53:14,873 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:14,874 /usr/local/include 2023-09-12T10:53:14,874 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:14,875 /usr/include 2023-09-12T10:53:14,875 End of search list. 2023-09-12T10:53:14,876 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:14,877 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:14,878 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:14,878 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:14,882 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:16,465 In file included from include/openbabel/atom.h:33, 2023-09-12T10:53:16,466 from include/openbabel/mol.h:43, 2023-09-12T10:53:16,466 from ./src/fingerprints/finger3.cpp:19: 2023-09-12T10:53:16,467 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:16,468 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:16,468 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:16,469 | ^ 2023-09-12T10:53:16,470 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:16,471 37 | # define UNUSED(x) x 2023-09-12T10:53:16,471 | ^ 2023-09-12T10:53:17,235 In file included from include/openbabel/mol.h:52: 2023-09-12T10:53:17,236 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:17,237 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:17,237 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:17,238 | ^ 2023-09-12T10:53:17,238 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:17,239 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:17,240 | ^~~~~~~~ 2023-09-12T10:53:17,249 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:17,250 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:17,250 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:17,251 | ^ 2023-09-12T10:53:17,251 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:17,252 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:17,253 | ^~~~~~~~ 2023-09-12T10:53:17,259 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:17,260 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:17,261 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:17,262 | ^ 2023-09-12T10:53:17,262 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:17,263 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:17,264 | ^~~~~~~~ 2023-09-12T10:53:17,266 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:17,267 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:17,267 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:17,268 | ^ 2023-09-12T10:53:17,269 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:17,270 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:17,271 | ^~~~~~~~ 2023-09-12T10:53:17,459 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:53:17,460 from ./src/fingerprints/finger3.cpp:26: 2023-09-12T10:53:17,461 include/openbabel/plugin.h: At global scope: 2023-09-12T10:53:17,461 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:53:17,462 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:53:17,462 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:17,463 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:53:17,463 from /usr/include/c++/12/vector:66, 2023-09-12T10:53:17,464 from include/openbabel/mol.h:35: 2023-09-12T10:53:17,465 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:53:17,465 131 | struct binary_function 2023-09-12T10:53:17,466 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:17,530 ./src/fingerprints/finger3.cpp: In member function ‘virtual bool OpenBabel::PatternFP::GetFingerprint(OpenBabel::OBBase*, std::vector&, int)’: 2023-09-12T10:53:17,530 ./src/fingerprints/finger3.cpp:108:13: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:17,531 108 | while(n < _bitcount) 2023-09-12T10:53:17,531 | ~~^~~~~~~~~~~ 2023-09-12T10:53:17,550 ./src/fingerprints/finger3.cpp: In member function ‘virtual std::string OpenBabel::PatternFP::DescribeBits(std::vector, bool)’: 2023-09-12T10:53:17,551 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2023-09-12T10:53:17,552 257 | ngrp = (num + div -1)/div--; //rounds up 2023-09-12T10:53:17,553 | ~~~^~ 2023-09-12T10:53:17,553 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2023-09-12T10:53:22,802 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:53:22,803 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/ccu3V50I.s 2023-09-12T10:53:22,807 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:23,241 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/ 2023-09-12T10:53:23,241 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/ 2023-09-12T10:53:23,242 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/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.' 2023-09-12T10:53:23,244 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 2023-09-12T10:53:23,248 Using built-in specs. 2023-09-12T10:53:23,249 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:23,250 Target: arm-linux-gnueabihf 2023-09-12T10:53:23,250 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 2023-09-12T10:53:23,251 Thread model: posix 2023-09-12T10:53:23,251 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:23,252 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:23,252 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/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/' 2023-09-12T10:53:23,253 /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/ccA5nmmF.s 2023-09-12T10:53:23,261 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:23,262 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:23,263 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:23,264 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:23,265 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:23,265 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:23,266 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:23,267 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:23,267 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:23,268 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:23,268 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:23,269 #include "..." search starts here: 2023-09-12T10:53:23,269 #include <...> search starts here: 2023-09-12T10:53:23,270 /usr/include/eigen3 2023-09-12T10:53:23,270 include 2023-09-12T10:53:23,271 /usr/include/python3.11 2023-09-12T10:53:23,271 /usr/include/c++/12 2023-09-12T10:53:23,271 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:23,272 /usr/include/c++/12/backward 2023-09-12T10:53:23,272 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:23,273 /usr/local/include 2023-09-12T10:53:23,273 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:23,274 /usr/include 2023-09-12T10:53:23,274 End of search list. 2023-09-12T10:53:23,275 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:23,275 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 2023-09-12T10:53:23,276 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:23,277 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:23,281 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:24,841 In file included from include/openbabel/atom.h:33, 2023-09-12T10:53:24,842 from include/openbabel/mol.h:43, 2023-09-12T10:53:24,843 from ./src/fingerprints/fingerecfp.cpp:15: 2023-09-12T10:53:24,843 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:24,844 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:24,845 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:24,846 | ^ 2023-09-12T10:53:24,846 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:24,847 37 | # define UNUSED(x) x 2023-09-12T10:53:24,848 | ^ 2023-09-12T10:53:25,613 In file included from include/openbabel/mol.h:52: 2023-09-12T10:53:25,614 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:25,614 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:25,616 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:25,616 | ^ 2023-09-12T10:53:25,617 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:25,618 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:25,618 | ^~~~~~~~ 2023-09-12T10:53:25,622 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:25,623 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:25,624 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:25,624 | ^ 2023-09-12T10:53:25,625 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:25,626 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:25,626 | ^~~~~~~~ 2023-09-12T10:53:25,644 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:25,645 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:25,645 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:25,646 | ^ 2023-09-12T10:53:25,646 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:25,647 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:25,647 | ^~~~~~~~ 2023-09-12T10:53:25,653 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:25,654 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:25,654 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:25,655 | ^ 2023-09-12T10:53:25,655 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:25,656 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:25,657 | ^~~~~~~~ 2023-09-12T10:53:25,848 In file included from include/openbabel/fingerprint.h:28, 2023-09-12T10:53:25,849 from ./src/fingerprints/fingerecfp.cpp:16: 2023-09-12T10:53:25,849 include/openbabel/plugin.h: At global scope: 2023-09-12T10:53:25,850 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:53:25,851 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:53:25,851 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:25,852 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:53:25,853 from /usr/include/c++/12/vector:66, 2023-09-12T10:53:25,853 from include/openbabel/mol.h:35: 2023-09-12T10:53:25,854 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:53:25,854 131 | struct binary_function 2023-09-12T10:53:25,855 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:25,905 ./src/fingerprints/fingerecfp.cpp: In member function ‘virtual std::string OpenBabel::fingerprintECFP::DescribeBits(std::vector, bool)’: 2023-09-12T10:53:25,905 ./src/fingerprints/fingerecfp.cpp:43:70: warning: unused parameter ‘fp’ [-Wunused-parameter] 2023-09-12T10:53:25,906 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:53:25,907 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2023-09-12T10:53:25,907 ./src/fingerprints/fingerecfp.cpp:43:79: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2023-09-12T10:53:25,908 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2023-09-12T10:53:25,909 | ~~~~~^~~~~~~~~ 2023-09-12T10:53:27,211 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(unsigned char*, unsigned int)’: 2023-09-12T10:53:27,211 ./src/fingerprints/fingerecfp.cpp:105:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,211 105 | case 11: c += ((unsigned int)ptr[10]<<24); 2023-09-12T10:53:27,212 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,212 ./src/fingerprints/fingerecfp.cpp:106:3: note: here 2023-09-12T10:53:27,213 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2023-09-12T10:53:27,213 | ^~~~ 2023-09-12T10:53:27,214 ./src/fingerprints/fingerecfp.cpp:106:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,214 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2023-09-12T10:53:27,215 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,215 ./src/fingerprints/fingerecfp.cpp:107:3: note: here 2023-09-12T10:53:27,216 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2023-09-12T10:53:27,216 | ^~~~ 2023-09-12T10:53:27,217 ./src/fingerprints/fingerecfp.cpp:107:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,217 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2023-09-12T10:53:27,218 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,218 ./src/fingerprints/fingerecfp.cpp:108:3: note: here 2023-09-12T10:53:27,219 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2023-09-12T10:53:27,219 | ^~~~ 2023-09-12T10:53:27,220 ./src/fingerprints/fingerecfp.cpp:108:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,220 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2023-09-12T10:53:27,220 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,221 ./src/fingerprints/fingerecfp.cpp:109:3: note: here 2023-09-12T10:53:27,222 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2023-09-12T10:53:27,222 | ^~~~ 2023-09-12T10:53:27,223 ./src/fingerprints/fingerecfp.cpp:109:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,224 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2023-09-12T10:53:27,225 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,225 ./src/fingerprints/fingerecfp.cpp:110:3: note: here 2023-09-12T10:53:27,226 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2023-09-12T10:53:27,227 | ^~~~ 2023-09-12T10:53:27,228 ./src/fingerprints/fingerecfp.cpp:110:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,228 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2023-09-12T10:53:27,229 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,229 ./src/fingerprints/fingerecfp.cpp:111:3: note: here 2023-09-12T10:53:27,230 111 | case 5: b += ptr[4]; 2023-09-12T10:53:27,231 | ^~~~ 2023-09-12T10:53:27,231 ./src/fingerprints/fingerecfp.cpp:111:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,232 111 | case 5: b += ptr[4]; 2023-09-12T10:53:27,233 | ~~^~~~~~~~~ 2023-09-12T10:53:27,233 ./src/fingerprints/fingerecfp.cpp:112:3: note: here 2023-09-12T10:53:27,234 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2023-09-12T10:53:27,235 | ^~~~ 2023-09-12T10:53:27,236 ./src/fingerprints/fingerecfp.cpp:112:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,236 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2023-09-12T10:53:27,237 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,238 ./src/fingerprints/fingerecfp.cpp:113:3: note: here 2023-09-12T10:53:27,239 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2023-09-12T10:53:27,240 | ^~~~ 2023-09-12T10:53:27,240 ./src/fingerprints/fingerecfp.cpp:113:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,241 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2023-09-12T10:53:27,241 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,242 ./src/fingerprints/fingerecfp.cpp:114:3: note: here 2023-09-12T10:53:27,242 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2023-09-12T10:53:27,243 | ^~~~ 2023-09-12T10:53:27,243 ./src/fingerprints/fingerecfp.cpp:114:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,244 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2023-09-12T10:53:27,244 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:27,245 ./src/fingerprints/fingerecfp.cpp:115:3: note: here 2023-09-12T10:53:27,245 115 | case 1: a += ptr[0]; 2023-09-12T10:53:27,246 | ^~~~ 2023-09-12T10:53:27,246 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(std::vector&)’: 2023-09-12T10:53:27,247 ./src/fingerprints/fingerecfp.cpp:139:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:53:27,247 139 | case 2: b += v[i+1]; 2023-09-12T10:53:27,248 ./src/fingerprints/fingerecfp.cpp:140:3: note: here 2023-09-12T10:53:27,248 140 | case 1: a += v[i]; 2023-09-12T10:53:27,249 | ^~~~ 2023-09-12T10:53:29,944 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/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/' 2023-09-12T10:53:29,944 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/ccA5nmmF.s 2023-09-12T10:53:29,949 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:30,163 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/ 2023-09-12T10:53:30,164 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/ 2023-09-12T10:53:30,165 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:53:30,166 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/forcefield.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefield.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:53:30,170 Using built-in specs. 2023-09-12T10:53:30,170 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:30,171 Target: arm-linux-gnueabihf 2023-09-12T10:53:30,171 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 2023-09-12T10:53:30,172 Thread model: posix 2023-09-12T10:53:30,172 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:30,173 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:30,173 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/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/' 2023-09-12T10:53:30,174 /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/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/cc20JObv.s 2023-09-12T10:53:30,182 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:30,183 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 2023-09-12T10:53:30,184 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:30,185 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:30,185 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:30,186 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:30,186 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:30,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:30,187 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:30,188 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:30,189 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:30,189 #include "..." search starts here: 2023-09-12T10:53:30,190 #include <...> search starts here: 2023-09-12T10:53:30,190 /usr/include/eigen3 2023-09-12T10:53:30,191 include 2023-09-12T10:53:30,192 /usr/include/python3.11 2023-09-12T10:53:30,192 /usr/include/c++/12 2023-09-12T10:53:30,193 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:30,194 /usr/include/c++/12/backward 2023-09-12T10:53:30,194 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:30,195 /usr/local/include 2023-09-12T10:53:30,195 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:30,196 /usr/include 2023-09-12T10:53:30,196 End of search list. 2023-09-12T10:53:30,197 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:30,197 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:30,198 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:30,198 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:30,206 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:31,745 In file included from include/openbabel/forcefield.h:30, 2023-09-12T10:53:31,745 from ./src/forcefield.cpp:22: 2023-09-12T10:53:31,746 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:31,747 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:31,747 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:31,748 | ^ 2023-09-12T10:53:31,748 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:31,749 37 | # define UNUSED(x) x 2023-09-12T10:53:31,750 | ^ 2023-09-12T10:53:32,557 In file included from include/openbabel/mol.h:52, 2023-09-12T10:53:32,558 from include/openbabel/forcefield.h:31: 2023-09-12T10:53:32,558 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:32,559 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:32,560 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:32,561 | ^ 2023-09-12T10:53:32,562 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:32,563 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:32,563 | ^~~~~~~~ 2023-09-12T10:53:32,564 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:32,565 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:32,566 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:32,566 | ^ 2023-09-12T10:53:32,567 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:32,568 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:32,568 | ^~~~~~~~ 2023-09-12T10:53:32,583 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:32,584 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:32,584 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:32,585 | ^ 2023-09-12T10:53:32,586 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:32,587 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:32,587 | ^~~~~~~~ 2023-09-12T10:53:32,590 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:32,590 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:32,591 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:32,591 | ^ 2023-09-12T10:53:32,592 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:32,593 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:32,593 | ^~~~~~~~ 2023-09-12T10:53:32,763 In file included from include/openbabel/forcefield.h:32: 2023-09-12T10:53:32,764 include/openbabel/plugin.h: At global scope: 2023-09-12T10:53:32,764 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:53:32,765 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:53:32,766 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:32,767 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:53:32,767 from /usr/include/c++/12/vector:66, 2023-09-12T10:53:32,768 from include/openbabel/forcefield.h:23: 2023-09-12T10:53:32,769 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:53:32,770 131 | struct binary_function 2023-09-12T10:53:32,770 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:32,891 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:53:32,891 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,892 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,893 | ^ 2023-09-12T10:53:32,894 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,894 37 | # define UNUSED(x) x 2023-09-12T10:53:32,895 | ^ 2023-09-12T10:53:32,896 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:53:32,896 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,897 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,898 | ^ 2023-09-12T10:53:32,898 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,899 37 | # define UNUSED(x) x 2023-09-12T10:53:32,900 | ^ 2023-09-12T10:53:32,901 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:53:32,902 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,902 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,903 | ^ 2023-09-12T10:53:32,904 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,905 37 | # define UNUSED(x) x 2023-09-12T10:53:32,905 | ^ 2023-09-12T10:53:32,906 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:53:32,906 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,907 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,907 | ^ 2023-09-12T10:53:32,908 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,909 37 | # define UNUSED(x) x 2023-09-12T10:53:32,909 | ^ 2023-09-12T10:53:32,910 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:53:32,910 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,911 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,911 | ^ 2023-09-12T10:53:32,912 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,912 37 | # define UNUSED(x) x 2023-09-12T10:53:32,913 | ^ 2023-09-12T10:53:32,914 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:53:32,914 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,915 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,916 | ^ 2023-09-12T10:53:32,916 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,917 37 | # define UNUSED(x) x 2023-09-12T10:53:32,918 | ^ 2023-09-12T10:53:32,918 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:53:32,919 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,920 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,921 | ^ 2023-09-12T10:53:32,921 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,922 37 | # define UNUSED(x) x 2023-09-12T10:53:32,923 | ^ 2023-09-12T10:53:32,923 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:53:32,924 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:32,924 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:32,925 | ^ 2023-09-12T10:53:32,926 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,926 37 | # define UNUSED(x) x 2023-09-12T10:53:32,927 | ^ 2023-09-12T10:53:32,944 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2023-09-12T10:53:32,945 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2023-09-12T10:53:32,946 417 | void SetDelta(double UNUSED(d)) {} 2023-09-12T10:53:32,947 | ^ 2023-09-12T10:53:32,948 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,948 37 | # define UNUSED(x) x 2023-09-12T10:53:32,949 | ^ 2023-09-12T10:53:32,949 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2023-09-12T10:53:32,950 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2023-09-12T10:53:32,950 433 | void SetNumCoords(int UNUSED(nc)) {} 2023-09-12T10:53:32,951 | ^ 2023-09-12T10:53:32,951 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:32,952 37 | # define UNUSED(x) x 2023-09-12T10:53:32,953 | ^ 2023-09-12T10:53:33,062 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int)’: 2023-09-12T10:53:33,063 ./src/forcefield.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:33,064 384 | if (_ignoreAtom == a) 2023-09-12T10:53:33,064 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:53:33,065 ./src/forcefield.cpp:386:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:33,065 386 | if (_ignoreAtom == b) 2023-09-12T10:53:33,066 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:53:33,067 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int)’: 2023-09-12T10:53:33,067 ./src/forcefield.cpp:396:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:33,068 396 | if (_ignoreAtom == b) 2023-09-12T10:53:33,068 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:53:33,069 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int, int)’: 2023-09-12T10:53:33,070 ./src/forcefield.cpp:406:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:53:33,071 406 | if (_ignoreAtom == d) 2023-09-12T10:53:33,071 | ~~~~~~~~~~~~^~~~ 2023-09-12T10:53:33,091 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintType(int) const’: 2023-09-12T10:53:33,092 ./src/forcefield.cpp:658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,093 658 | if (index >= _constraints.size()) 2023-09-12T10:53:33,094 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,094 ./src/forcefield.cpp: In member function ‘double OpenBabel::OBFFConstraints::GetConstraintValue(int) const’: 2023-09-12T10:53:33,095 ./src/forcefield.cpp:666:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,096 666 | if (index >= _constraints.size()) 2023-09-12T10:53:33,096 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,097 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomA(int) const’: 2023-09-12T10:53:33,098 ./src/forcefield.cpp:674:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,098 674 | if (index >= _constraints.size()) 2023-09-12T10:53:33,099 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,100 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomB(int) const’: 2023-09-12T10:53:33,101 ./src/forcefield.cpp:682:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,102 682 | if (index >= _constraints.size()) 2023-09-12T10:53:33,103 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,103 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomC(int) const’: 2023-09-12T10:53:33,104 ./src/forcefield.cpp:690:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,104 690 | if (index >= _constraints.size()) 2023-09-12T10:53:33,105 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,105 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomD(int) const’: 2023-09-12T10:53:33,106 ./src/forcefield.cpp:698:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,107 698 | if (index >= _constraints.size()) 2023-09-12T10:53:33,107 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,158 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2023-09-12T10:53:33,159 ./src/forcefield.cpp:1358:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2023-09-12T10:53:33,159 1358 | num_permutations = factorial[num_rotors_to_permute]; 2023-09-12T10:53:33,160 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:33,161 ./src/forcefield.cpp:1362:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,161 1362 | for (int i=0; i::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T10:53:33,184 1375 | for (int i=0; i >&, std::vector, double)’: 2023-09-12T10:53:33,208 ./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] 2023-09-12T10:53:33,209 1576 | if (j == rotorKey[i]) 2023-09-12T10:53:33,210 ./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] 2023-09-12T10:53:33,211 1595 | if (j == rotorKey[i]) 2023-09-12T10:53:33,236 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::DistanceGeometry()’: 2023-09-12T10:53:33,237 ./src/forcefield.cpp:1975:26: warning: variable ‘l_bc’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:53:33,238 1975 | double l_ab, l_bc, l_ac; // lower limits 2023-09-12T10:53:33,238 | ^~~~ 2023-09-12T10:53:33,288 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::SteepestDescentInitialize(int, double, int)’: 2023-09-12T10:53:33,289 ./src/forcefield.cpp:2747:77: warning: unused parameter ‘method’ [-Wunused-parameter] 2023-09-12T10:53:33,289 2747 | void OBForceField::SteepestDescentInitialize(int steps, double econv, int method) 2023-09-12T10:53:33,290 | ~~~~^~~~~~ 2023-09-12T10:53:33,299 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ConjugateGradientsInitialize(int, double, int)’: 2023-09-12T10:53:33,300 ./src/forcefield.cpp:2873:55: warning: unused parameter ‘method’ [-Wunused-parameter] 2023-09-12T10:53:33,300 2873 | int method) 2023-09-12T10:53:33,301 | ~~~~^~~~~~ 2023-09-12T10:53:33,339 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::MolecularDynamicsTakeNSteps(int, double, double, int)’: 2023-09-12T10:53:33,340 ./src/forcefield.cpp:3524:88: warning: unused parameter ‘method’ [-Wunused-parameter] 2023-09-12T10:53:33,340 3524 | void OBForceField::MolecularDynamicsTakeNSteps(int n, double T, double timestep, int method) 2023-09-12T10:53:33,341 | ~~~~^~~~~~ 2023-09-12T10:53:46,747 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:53:46,747 /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]’: 2023-09-12T10:53:46,748 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:46,749 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:46,749 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:46,864 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:46,865 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, 2023-09-12T10:53:46,865 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, 2023-09-12T10:53:46,866 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, 2023-09-12T10:53:46,867 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2023-09-12T10:53:46,867 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:46,868 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:46,868 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:46,869 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2023-09-12T10:53:46,870 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2023-09-12T10:53:46,870 645 | OBFFConstraint constraint; 2023-09-12T10:53:46,872 | ^~~~~~~~~~ 2023-09-12T10:53:46,872 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:46,872 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, 2023-09-12T10:53:46,873 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, 2023-09-12T10:53:46,873 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, 2023-09-12T10:53:46,874 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2023-09-12T10:53:46,874 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:46,874 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:46,875 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:46,875 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2023-09-12T10:53:46,876 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2023-09-12T10:53:46,877 645 | OBFFConstraint constraint; 2023-09-12T10:53:46,877 | ^~~~~~~~~~ 2023-09-12T10:53:46,878 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:53:46,879 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:46,879 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2023-09-12T10:53:46,880 /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 2023-09-12T10:53:46,881 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:46,881 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:46,917 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:46,918 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, 2023-09-12T10:53:46,918 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, 2023-09-12T10:53:46,919 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, 2023-09-12T10:53:46,920 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2023-09-12T10:53:46,920 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:46,921 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:46,922 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:46,922 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2023-09-12T10:53:46,923 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2023-09-12T10:53:46,923 570 | OBFFConstraint constraint; 2023-09-12T10:53:46,924 | ^~~~~~~~~~ 2023-09-12T10:53:46,924 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:46,925 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, 2023-09-12T10:53:46,925 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, 2023-09-12T10:53:46,926 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, 2023-09-12T10:53:46,926 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2023-09-12T10:53:46,927 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:46,927 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:46,928 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:46,928 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2023-09-12T10:53:46,929 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2023-09-12T10:53:46,930 570 | OBFFConstraint constraint; 2023-09-12T10:53:46,930 | ^~~~~~~~~~ 2023-09-12T10:53:46,931 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:46,932 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2023-09-12T10:53:46,933 /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 2023-09-12T10:53:46,933 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:46,934 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:46,971 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:46,972 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, 2023-09-12T10:53:46,972 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, 2023-09-12T10:53:46,973 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, 2023-09-12T10:53:46,973 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2023-09-12T10:53:46,974 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:46,975 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:46,976 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:46,976 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2023-09-12T10:53:46,977 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2023-09-12T10:53:46,977 580 | OBFFConstraint constraint; 2023-09-12T10:53:46,978 | ^~~~~~~~~~ 2023-09-12T10:53:46,978 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:46,979 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, 2023-09-12T10:53:46,979 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, 2023-09-12T10:53:46,980 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, 2023-09-12T10:53:46,980 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2023-09-12T10:53:46,981 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:46,981 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:46,982 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:46,983 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2023-09-12T10:53:46,983 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2023-09-12T10:53:46,984 580 | OBFFConstraint constraint; 2023-09-12T10:53:46,984 | ^~~~~~~~~~ 2023-09-12T10:53:46,985 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:46,985 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2023-09-12T10:53:46,986 /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 2023-09-12T10:53:46,987 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:46,987 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:47,026 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,027 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, 2023-09-12T10:53:47,027 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, 2023-09-12T10:53:47,028 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, 2023-09-12T10:53:47,029 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2023-09-12T10:53:47,030 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,031 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,031 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,032 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2023-09-12T10:53:47,032 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,033 602 | OBFFConstraint constraint; 2023-09-12T10:53:47,034 | ^~~~~~~~~~ 2023-09-12T10:53:47,034 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,035 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, 2023-09-12T10:53:47,035 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, 2023-09-12T10:53:47,036 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, 2023-09-12T10:53:47,036 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2023-09-12T10:53:47,037 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,037 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,038 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,038 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2023-09-12T10:53:47,039 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,040 602 | OBFFConstraint constraint; 2023-09-12T10:53:47,040 | ^~~~~~~~~~ 2023-09-12T10:53:47,041 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:47,042 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2023-09-12T10:53:47,042 /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 2023-09-12T10:53:47,043 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:47,044 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:47,078 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,079 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, 2023-09-12T10:53:47,079 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, 2023-09-12T10:53:47,080 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, 2023-09-12T10:53:47,081 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2023-09-12T10:53:47,082 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,082 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,083 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,083 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2023-09-12T10:53:47,084 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,084 591 | OBFFConstraint constraint; 2023-09-12T10:53:47,085 | ^~~~~~~~~~ 2023-09-12T10:53:47,085 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,085 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, 2023-09-12T10:53:47,086 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, 2023-09-12T10:53:47,086 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, 2023-09-12T10:53:47,087 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2023-09-12T10:53:47,088 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,088 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,089 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,089 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2023-09-12T10:53:47,090 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,091 591 | OBFFConstraint constraint; 2023-09-12T10:53:47,091 | ^~~~~~~~~~ 2023-09-12T10:53:47,092 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:47,093 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2023-09-12T10:53:47,094 /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 2023-09-12T10:53:47,094 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:47,095 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:47,132 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,133 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, 2023-09-12T10:53:47,134 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, 2023-09-12T10:53:47,134 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, 2023-09-12T10:53:47,135 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2023-09-12T10:53:47,136 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,136 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,137 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,137 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2023-09-12T10:53:47,138 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,138 622 | OBFFConstraint constraint; 2023-09-12T10:53:47,139 | ^~~~~~~~~~ 2023-09-12T10:53:47,139 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,140 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, 2023-09-12T10:53:47,140 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, 2023-09-12T10:53:47,141 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, 2023-09-12T10:53:47,141 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2023-09-12T10:53:47,142 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,142 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,143 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,144 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2023-09-12T10:53:47,145 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,146 622 | OBFFConstraint constraint; 2023-09-12T10:53:47,146 | ^~~~~~~~~~ 2023-09-12T10:53:47,147 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:47,147 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2023-09-12T10:53:47,148 /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 2023-09-12T10:53:47,149 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:47,149 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:47,185 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,186 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, 2023-09-12T10:53:47,186 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, 2023-09-12T10:53:47,187 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, 2023-09-12T10:53:47,188 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2023-09-12T10:53:47,188 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,189 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,189 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,190 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2023-09-12T10:53:47,190 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,191 613 | OBFFConstraint constraint; 2023-09-12T10:53:47,191 | ^~~~~~~~~~ 2023-09-12T10:53:47,192 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,192 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, 2023-09-12T10:53:47,193 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, 2023-09-12T10:53:47,193 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, 2023-09-12T10:53:47,194 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2023-09-12T10:53:47,194 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,195 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,196 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,196 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2023-09-12T10:53:47,197 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,197 613 | OBFFConstraint constraint; 2023-09-12T10:53:47,198 | ^~~~~~~~~~ 2023-09-12T10:53:47,199 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:47,199 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2023-09-12T10:53:47,200 /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 2023-09-12T10:53:47,200 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:47,201 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:47,237 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,237 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, 2023-09-12T10:53:47,238 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, 2023-09-12T10:53:47,239 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, 2023-09-12T10:53:47,240 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2023-09-12T10:53:47,240 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,240 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,241 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,241 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2023-09-12T10:53:47,242 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,242 633 | OBFFConstraint constraint; 2023-09-12T10:53:47,243 | ^~~~~~~~~~ 2023-09-12T10:53:47,243 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2023-09-12T10:53:47,244 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, 2023-09-12T10:53:47,244 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, 2023-09-12T10:53:47,245 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, 2023-09-12T10:53:47,246 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2023-09-12T10:53:47,246 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,247 235 | class OBFPRT OBFFConstraint 2023-09-12T10:53:47,248 | ^~~~~~~~~~~~~~ 2023-09-12T10:53:47,248 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2023-09-12T10:53:47,249 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2023-09-12T10:53:47,249 633 | OBFFConstraint constraint; 2023-09-12T10:53:47,250 | ^~~~~~~~~~ 2023-09-12T10:53:47,251 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’, 2023-09-12T10:53:47,251 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2023-09-12T10:53:47,252 /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 2023-09-12T10:53:47,252 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:47,253 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:47,874 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2023-09-12T10:53:47,874 ./src/forcefield.cpp:1415:11: warning: ‘minE’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,875 1415 | if (minE < best_minE) { 2023-09-12T10:53:47,876 | ^~ 2023-09-12T10:53:47,876 ./src/forcefield.cpp:1325:22: note: ‘minE’ was declared here 2023-09-12T10:53:47,877 1325 | double currentE, minE, best_minE; 2023-09-12T10:53:47,877 | ^~~~ 2023-09-12T10:53:47,878 ./src/forcefield.cpp:1398:29: warning: ‘minj’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:53:47,879 1398 | rotorKey[idx + 1] = minj; 2023-09-12T10:53:47,879 | ^~~~ 2023-09-12T10:53:47,880 ./src/forcefield.cpp:1324:21: note: ‘minj’ was declared here 2023-09-12T10:53:47,880 1324 | unsigned int j, minj; 2023-09-12T10:53:47,881 | ^~~~ 2023-09-12T10:53:48,637 /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]’: 2023-09-12T10:53:48,637 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:48,638 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:53:48,639 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,285 /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]’: 2023-09-12T10:53:49,286 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:49,347 /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]’: 2023-09-12T10:53:49,347 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:53:49,407 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:49,407 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, 2023-09-12T10:53:49,408 inlined from ‘bool OpenBabel::OBForceField::RandomRotorSearchNextConformer(unsigned int)’ at ./src/forcefield.cpp:1540:24: 2023-09-12T10:53:49,409 /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 2023-09-12T10:53:49,409 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:49,410 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,487 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:49,488 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, 2023-09-12T10:53:49,489 inlined from ‘bool OpenBabel::OBForceField::SystematicRotorSearchNextConformer(unsigned int)’ at ./src/forcefield.cpp:1274:24: 2023-09-12T10:53:49,489 /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 2023-09-12T10:53:49,490 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:49,491 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,993 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:49,993 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, 2023-09-12T10:53:49,994 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1660:26: 2023-09-12T10:53:49,995 /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 2023-09-12T10:53:49,995 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:49,996 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:49,996 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:49,997 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, 2023-09-12T10:53:49,998 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1665:24: 2023-09-12T10:53:49,998 /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 2023-09-12T10:53:49,999 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:50,000 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:50,000 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:50,001 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1714:27: 2023-09-12T10:53:50,002 /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 2023-09-12T10:53:50,003 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:50,003 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:50,004 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:50,005 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1733:28: 2023-09-12T10:53:50,005 /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 2023-09-12T10:53:50,006 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:50,007 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:50,007 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:53:50,008 inlined from ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’ at ./src/forcefield.cpp:1790:26: 2023-09-12T10:53:50,009 /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 2023-09-12T10:53:50,010 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:53:50,011 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:53:51,167 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:53:51,167 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, 2023-09-12T10:53:51,168 inlined from ‘bool OpenBabel::OBForceField::GetCoordinates(OpenBabel::OBMol&)’ at ./src/forcefield.cpp:1049:23: 2023-09-12T10:53:51,168 /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 2023-09-12T10:53:51,169 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:53:51,169 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:53:52,802 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:53:52,803 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/cc20JObv.s 2023-09-12T10:53:52,807 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:53:54,126 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/ 2023-09-12T10:53:54,127 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/ 2023-09-12T10:53:54,128 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/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.' 2023-09-12T10:53:54,133 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 2023-09-12T10:53:54,137 Using built-in specs. 2023-09-12T10:53:54,138 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:53:54,138 Target: arm-linux-gnueabihf 2023-09-12T10:53:54,139 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 2023-09-12T10:53:54,140 Thread model: posix 2023-09-12T10:53:54,141 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:53:54,141 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:53:54,142 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/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/' 2023-09-12T10:53:54,142 /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/cc9Re9Bh.s 2023-09-12T10:53:54,151 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:54,151 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:54,153 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:54,153 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:54,154 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:53:54,154 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:53:54,155 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:53:54,156 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:53:54,156 ignoring duplicate directory "/usr/include/" 2023-09-12T10:53:54,157 as it is a non-system directory that duplicates a system directory 2023-09-12T10:53:54,158 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:53:54,158 #include "..." search starts here: 2023-09-12T10:53:54,159 #include <...> search starts here: 2023-09-12T10:53:54,159 /usr/include/eigen3 2023-09-12T10:53:54,160 include 2023-09-12T10:53:54,160 /usr/include/python3.11 2023-09-12T10:53:54,161 /usr/include/c++/12 2023-09-12T10:53:54,161 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:53:54,162 /usr/include/c++/12/backward 2023-09-12T10:53:54,163 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:53:54,163 /usr/local/include 2023-09-12T10:53:54,164 /usr/include/arm-linux-gnueabihf 2023-09-12T10:53:54,164 /usr/include 2023-09-12T10:53:54,165 End of search list. 2023-09-12T10:53:54,166 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:53:54,167 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:53:54,168 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:53:54,168 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:53:54,173 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:53:55,747 In file included from include/openbabel/atom.h:33, 2023-09-12T10:53:55,748 from include/openbabel/mol.h:43, 2023-09-12T10:53:55,748 from ./src/forcefields/forcefieldgaff.cpp:21: 2023-09-12T10:53:55,749 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:53:55,750 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:53:55,750 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:53:55,751 | ^ 2023-09-12T10:53:55,751 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:55,752 37 | # define UNUSED(x) x 2023-09-12T10:53:55,752 | ^ 2023-09-12T10:53:56,515 In file included from include/openbabel/mol.h:52: 2023-09-12T10:53:56,516 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:56,516 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:56,517 862 | {return new OBVibrationData(*this);} 2023-09-12T10:53:56,517 | ^ 2023-09-12T10:53:56,518 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:53:56,519 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:53:56,520 | ^~~~~~~~ 2023-09-12T10:53:56,521 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:56,522 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:56,522 907 | {return new OBDOSData(*this);} 2023-09-12T10:53:56,523 | ^ 2023-09-12T10:53:56,524 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:53:56,524 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:53:56,525 | ^~~~~~~~ 2023-09-12T10:53:56,540 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:56,540 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:56,541 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:53:56,542 | ^ 2023-09-12T10:53:56,543 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:53:56,543 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:53:56,544 | ^~~~~~~~ 2023-09-12T10:53:56,546 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:53:56,547 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:53:56,548 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:53:56,548 | ^ 2023-09-12T10:53:56,549 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:53:56,549 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:53:56,550 | ^~~~~~~~ 2023-09-12T10:53:56,862 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:53:56,863 from include/forcefields/forcefieldgaff.h:24, 2023-09-12T10:53:56,863 from ./src/forcefields/forcefieldgaff.cpp:24: 2023-09-12T10:53:56,864 include/openbabel/plugin.h: At global scope: 2023-09-12T10:53:56,865 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:53:56,865 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:53:56,866 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:56,866 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:53:56,867 from /usr/include/c++/12/vector:66, 2023-09-12T10:53:56,868 from include/openbabel/mol.h:35: 2023-09-12T10:53:56,868 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:53:56,869 131 | struct binary_function 2023-09-12T10:53:56,870 | ^~~~~~~~~~~~~~~ 2023-09-12T10:53:56,991 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:53:56,992 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:56,993 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:56,994 | ^ 2023-09-12T10:53:56,994 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:56,995 37 | # define UNUSED(x) x 2023-09-12T10:53:56,996 | ^ 2023-09-12T10:53:56,997 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:53:56,997 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:56,998 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:56,999 | ^ 2023-09-12T10:53:56,999 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,000 37 | # define UNUSED(x) x 2023-09-12T10:53:57,001 | ^ 2023-09-12T10:53:57,001 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:53:57,002 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:57,003 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:57,004 | ^ 2023-09-12T10:53:57,005 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,006 37 | # define UNUSED(x) x 2023-09-12T10:53:57,006 | ^ 2023-09-12T10:53:57,007 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:53:57,007 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:57,008 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:57,008 | ^ 2023-09-12T10:53:57,009 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,009 37 | # define UNUSED(x) x 2023-09-12T10:53:57,010 | ^ 2023-09-12T10:53:57,010 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:53:57,011 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:57,012 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:57,012 | ^ 2023-09-12T10:53:57,013 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,013 37 | # define UNUSED(x) x 2023-09-12T10:53:57,014 | ^ 2023-09-12T10:53:57,014 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:53:57,015 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:57,016 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:57,016 | ^ 2023-09-12T10:53:57,017 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,017 37 | # define UNUSED(x) x 2023-09-12T10:53:57,018 | ^ 2023-09-12T10:53:57,019 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:53:57,019 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:57,020 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:57,021 | ^ 2023-09-12T10:53:57,021 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,022 37 | # define UNUSED(x) x 2023-09-12T10:53:57,023 | ^ 2023-09-12T10:53:57,023 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:53:57,024 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:53:57,025 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:53:57,025 | ^ 2023-09-12T10:53:57,026 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:53:57,026 37 | # define UNUSED(x) x 2023-09-12T10:53:57,027 | ^ 2023-09-12T10:54:04,856 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:54:04,857 /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]’: 2023-09-12T10:54:04,857 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:04,858 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:04,859 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:05,002 /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]’: 2023-09-12T10:54:05,002 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:05,191 /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]’: 2023-09-12T10:54:05,192 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:05,378 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:54:05,379 /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]’: 2023-09-12T10:54:05,379 /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 2023-09-12T10:54:05,380 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:05,380 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:05,482 /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]’: 2023-09-12T10:54:05,482 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:05,483 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:05,484 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:05,668 /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]’: 2023-09-12T10:54:05,668 /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 2023-09-12T10:54:05,669 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:05,669 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:05,759 /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]’: 2023-09-12T10:54:05,760 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:05,761 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:05,762 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:05,903 /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]’: 2023-09-12T10:54:05,904 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:06,759 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,759 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:54:06,760 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, 2023-09-12T10:54:06,761 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, 2023-09-12T10:54:06,761 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, 2023-09-12T10:54:06,762 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:54:06,762 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,763 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,764 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,764 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,765 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,766 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,766 | ^~~~~~~~ 2023-09-12T10:54:06,767 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,768 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:54:06,768 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, 2023-09-12T10:54:06,769 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, 2023-09-12T10:54:06,770 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, 2023-09-12T10:54:06,771 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:54:06,771 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,772 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,773 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,774 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,774 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,775 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,775 | ^~~~~~~~ 2023-09-12T10:54:06,776 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,777 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:54:06,777 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, 2023-09-12T10:54:06,778 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, 2023-09-12T10:54:06,778 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, 2023-09-12T10:54:06,779 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:54:06,780 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,780 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,781 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,782 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,782 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,783 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,784 | ^~~~~~~~ 2023-09-12T10:54:06,784 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:54:06,785 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, 2023-09-12T10:54:06,785 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, 2023-09-12T10:54:06,786 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, 2023-09-12T10:54:06,786 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:54:06,787 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,788 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:54:06,788 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,788 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,789 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,789 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,790 | ^~~~~~~~ 2023-09-12T10:54:06,790 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:54:06,790 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, 2023-09-12T10:54:06,791 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, 2023-09-12T10:54:06,791 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, 2023-09-12T10:54:06,792 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:54:06,792 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,793 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:54:06,793 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,794 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,794 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,795 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,796 | ^~~~~~~~ 2023-09-12T10:54:06,796 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,797 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:54:06,797 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, 2023-09-12T10:54:06,798 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, 2023-09-12T10:54:06,799 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, 2023-09-12T10:54:06,799 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:54:06,800 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,801 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,801 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,802 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,802 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,802 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,803 | ^~~~~~~~ 2023-09-12T10:54:06,803 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,804 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:54:06,804 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, 2023-09-12T10:54:06,805 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, 2023-09-12T10:54:06,805 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, 2023-09-12T10:54:06,805 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:54:06,806 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,806 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,807 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,807 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,808 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,809 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,809 | ^~~~~~~~ 2023-09-12T10:54:06,810 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,810 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2023-09-12T10:54:06,811 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, 2023-09-12T10:54:06,811 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, 2023-09-12T10:54:06,812 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, 2023-09-12T10:54:06,812 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:54:06,813 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,814 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,814 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,814 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,815 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,815 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,815 | ^~~~~~~~ 2023-09-12T10:54:06,816 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:54:06,816 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, 2023-09-12T10:54:06,816 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, 2023-09-12T10:54:06,817 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, 2023-09-12T10:54:06,817 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:54:06,818 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,818 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:54:06,819 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,819 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,820 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,821 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,821 | ^~~~~~~~ 2023-09-12T10:54:06,822 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’, 2023-09-12T10:54:06,822 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, 2023-09-12T10:54:06,823 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, 2023-09-12T10:54:06,823 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, 2023-09-12T10:54:06,824 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:54:06,824 include/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,825 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 2023-09-12T10:54:06,825 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,826 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,826 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2023-09-12T10:54:06,826 528 | OBFFBondCalculationGaff bondcalc; 2023-09-12T10:54:06,827 | ^~~~~~~~ 2023-09-12T10:54:06,827 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,828 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,828 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,829 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, 2023-09-12T10:54:06,829 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, 2023-09-12T10:54:06,830 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, 2023-09-12T10:54:06,831 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:54:06,831 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,832 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,833 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,834 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,834 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,835 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,836 | ^~~~~~~~~ 2023-09-12T10:54:06,837 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,837 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,838 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,839 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, 2023-09-12T10:54:06,840 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, 2023-09-12T10:54:06,841 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, 2023-09-12T10:54:06,841 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:54:06,842 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,843 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,843 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,844 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,844 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,845 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,846 | ^~~~~~~~~ 2023-09-12T10:54:06,846 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,847 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,848 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,849 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, 2023-09-12T10:54:06,849 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, 2023-09-12T10:54:06,850 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, 2023-09-12T10:54:06,851 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:54:06,852 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,852 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,853 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,854 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,854 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,855 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,856 | ^~~~~~~~~ 2023-09-12T10:54:06,857 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:06,858 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,858 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, 2023-09-12T10:54:06,859 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, 2023-09-12T10:54:06,860 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, 2023-09-12T10:54:06,860 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:54:06,861 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,861 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:06,862 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,863 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,863 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,864 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,865 | ^~~~~~~~~ 2023-09-12T10:54:06,866 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:54:06,867 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, 2023-09-12T10:54:06,867 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, 2023-09-12T10:54:06,868 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, 2023-09-12T10:54:06,869 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:54:06,870 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,870 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:54:06,871 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,872 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,873 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,873 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,874 | ^~~~~~~~~ 2023-09-12T10:54:06,875 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:54:06,875 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, 2023-09-12T10:54:06,876 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, 2023-09-12T10:54:06,877 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, 2023-09-12T10:54:06,877 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:54:06,878 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,878 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:54:06,879 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,880 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,880 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,881 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,882 | ^~~~~~~~~ 2023-09-12T10:54:06,883 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,883 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,884 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,885 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, 2023-09-12T10:54:06,886 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, 2023-09-12T10:54:06,886 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, 2023-09-12T10:54:06,887 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:54:06,888 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,889 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,890 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,890 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,891 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,891 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,892 | ^~~~~~~~~ 2023-09-12T10:54:06,892 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,893 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,893 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,894 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, 2023-09-12T10:54:06,895 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, 2023-09-12T10:54:06,895 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, 2023-09-12T10:54:06,896 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:54:06,896 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,897 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,898 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,899 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,899 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,900 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,901 | ^~~~~~~~~ 2023-09-12T10:54:06,901 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,902 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,903 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,904 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, 2023-09-12T10:54:06,904 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, 2023-09-12T10:54:06,905 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, 2023-09-12T10:54:06,906 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:54:06,907 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,907 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,908 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,908 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,909 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,909 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,910 | ^~~~~~~~~ 2023-09-12T10:54:06,910 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:06,911 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2023-09-12T10:54:06,912 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, 2023-09-12T10:54:06,912 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, 2023-09-12T10:54:06,913 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, 2023-09-12T10:54:06,913 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:54:06,914 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,915 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:06,916 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,916 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,917 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,918 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,918 | ^~~~~~~~~ 2023-09-12T10:54:06,919 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:54:06,920 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, 2023-09-12T10:54:06,920 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, 2023-09-12T10:54:06,921 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, 2023-09-12T10:54:06,922 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:54:06,923 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,923 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:54:06,924 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,924 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,925 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,925 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,926 | ^~~~~~~~~ 2023-09-12T10:54:06,926 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’, 2023-09-12T10:54:06,927 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, 2023-09-12T10:54:06,928 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, 2023-09-12T10:54:06,928 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, 2023-09-12T10:54:06,929 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:54:06,930 include/forcefields/forcefieldgaff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,931 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 2023-09-12T10:54:06,932 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,933 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,933 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2023-09-12T10:54:06,934 589 | OBFFAngleCalculationGaff anglecalc; 2023-09-12T10:54:06,935 | ^~~~~~~~~ 2023-09-12T10:54:06,935 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,936 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,937 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:06,938 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:54:06,939 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, 2023-09-12T10:54:06,940 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, 2023-09-12T10:54:06,941 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, 2023-09-12T10:54:06,941 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:54:06,942 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,942 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,943 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,943 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,944 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:54:06,945 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:54:06,945 | ^~~~~~~~~~~ 2023-09-12T10:54:06,946 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,947 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,948 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:06,949 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:54:06,949 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, 2023-09-12T10:54:06,950 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, 2023-09-12T10:54:06,951 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, 2023-09-12T10:54:06,952 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:54:06,952 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,953 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,954 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,954 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,955 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:54:06,955 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:54:06,956 | ^~~~~~~~~~~ 2023-09-12T10:54:06,956 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,957 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,957 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:06,958 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:54:06,958 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, 2023-09-12T10:54:06,959 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, 2023-09-12T10:54:06,959 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, 2023-09-12T10:54:06,960 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:54:06,961 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,961 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:06,962 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,963 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,964 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:54:06,965 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:54:06,965 | ^~~~~~~~~~~ 2023-09-12T10:54:06,966 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:06,967 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:06,967 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:54:06,968 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, 2023-09-12T10:54:06,968 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, 2023-09-12T10:54:06,969 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, 2023-09-12T10:54:06,970 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:54:06,971 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,971 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:06,972 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,973 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,973 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:54:06,974 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:54:06,974 | ^~~~~~~~~~~ 2023-09-12T10:54:06,975 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:54:06,976 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2023-09-12T10:54:06,977 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, 2023-09-12T10:54:06,978 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, 2023-09-12T10:54:06,979 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, 2023-09-12T10:54:06,980 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:54:06,981 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,981 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:54:06,982 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,983 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,983 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:54:06,984 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:54:06,985 | ^~~~~~~~~~~ 2023-09-12T10:54:06,985 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’, 2023-09-12T10:54:06,986 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, 2023-09-12T10:54:06,987 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, 2023-09-12T10:54:06,987 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, 2023-09-12T10:54:06,988 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:54:06,988 include/forcefields/forcefieldgaff.h:47:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,989 47 | class OBFFTorsionCalculationGaff : public OBFFCalculation4 2023-09-12T10:54:06,989 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:06,990 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:06,990 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2023-09-12T10:54:06,991 655 | OBFFTorsionCalculationGaff torsioncalc; 2023-09-12T10:54:06,992 | ^~~~~~~~~~~ 2023-09-12T10:54:06,993 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:06,993 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:06,994 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:06,995 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:06,996 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, 2023-09-12T10:54:06,996 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, 2023-09-12T10:54:06,997 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, 2023-09-12T10:54:06,998 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:54:06,999 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:06,999 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:07,000 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,001 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,002 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,003 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,003 | ^~~~~~~ 2023-09-12T10:54:07,004 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:07,004 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:07,004 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:07,005 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,005 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, 2023-09-12T10:54:07,006 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, 2023-09-12T10:54:07,006 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, 2023-09-12T10:54:07,007 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:54:07,007 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,008 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:07,009 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,009 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,010 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,011 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,011 | ^~~~~~~ 2023-09-12T10:54:07,012 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:07,012 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:07,013 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:07,013 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,014 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, 2023-09-12T10:54:07,015 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, 2023-09-12T10:54:07,015 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, 2023-09-12T10:54:07,016 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:54:07,017 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,017 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:07,018 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,018 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,019 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,019 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,020 | ^~~~~~~ 2023-09-12T10:54:07,020 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:07,021 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:07,021 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,022 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, 2023-09-12T10:54:07,022 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, 2023-09-12T10:54:07,023 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, 2023-09-12T10:54:07,024 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:54:07,025 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,025 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:07,026 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,027 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,027 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,028 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,029 | ^~~~~~~ 2023-09-12T10:54:07,029 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:54:07,030 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,031 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, 2023-09-12T10:54:07,032 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, 2023-09-12T10:54:07,032 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, 2023-09-12T10:54:07,033 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:54:07,033 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,034 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:54:07,034 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,035 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,035 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,036 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,036 | ^~~~~~~ 2023-09-12T10:54:07,037 In copy constructor ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’, 2023-09-12T10:54:07,037 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, 2023-09-12T10:54:07,038 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, 2023-09-12T10:54:07,038 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, 2023-09-12T10:54:07,039 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:54:07,039 include/forcefields/forcefieldgaff.h:55:9: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,040 55 | class OBFFOOPCalculationGaff : public OBFFCalculation4 2023-09-12T10:54:07,041 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,041 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,042 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,042 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,043 | ^~~~~~~ 2023-09-12T10:54:07,044 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:07,044 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:07,045 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:07,046 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,047 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, 2023-09-12T10:54:07,047 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, 2023-09-12T10:54:07,048 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, 2023-09-12T10:54:07,048 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:54:07,049 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,050 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:07,050 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,051 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,052 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,052 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,053 | ^~~~~~~ 2023-09-12T10:54:07,054 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:07,055 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:07,056 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:07,056 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,057 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, 2023-09-12T10:54:07,058 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, 2023-09-12T10:54:07,059 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, 2023-09-12T10:54:07,059 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:54:07,060 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,061 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:07,061 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,062 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,062 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,063 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,064 | ^~~~~~~ 2023-09-12T10:54:07,064 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:07,065 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:07,065 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:07,066 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,067 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, 2023-09-12T10:54:07,067 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, 2023-09-12T10:54:07,068 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, 2023-09-12T10:54:07,069 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:54:07,069 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,070 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:07,071 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,072 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,073 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,073 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,074 | ^~~~~~~ 2023-09-12T10:54:07,074 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:07,075 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:07,076 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,076 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, 2023-09-12T10:54:07,077 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, 2023-09-12T10:54:07,078 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, 2023-09-12T10:54:07,078 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:54:07,079 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,080 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:07,080 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,081 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,081 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,082 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,082 | ^~~~~~~ 2023-09-12T10:54:07,083 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:54:07,084 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2023-09-12T10:54:07,084 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, 2023-09-12T10:54:07,085 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, 2023-09-12T10:54:07,086 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, 2023-09-12T10:54:07,087 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:54:07,088 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,088 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:54:07,089 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,090 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,090 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,091 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,092 | ^~~~~~~ 2023-09-12T10:54:07,093 In copy constructor ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’, 2023-09-12T10:54:07,094 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, 2023-09-12T10:54:07,094 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, 2023-09-12T10:54:07,095 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, 2023-09-12T10:54:07,096 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:54:07,096 include/forcefields/forcefieldgaff.h:55:9: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:07,097 55 | class OBFFOOPCalculationGaff : public OBFFCalculation4 2023-09-12T10:54:07,097 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:07,098 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2023-09-12T10:54:07,098 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2023-09-12T10:54:07,099 726 | OBFFOOPCalculationGaff oopcalc; 2023-09-12T10:54:07,100 | ^~~~~~~ 2023-09-12T10:54:07,101 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,102 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2023-09-12T10:54:07,102 /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 2023-09-12T10:54:07,103 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,104 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,105 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,105 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2023-09-12T10:54:07,106 /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 2023-09-12T10:54:07,106 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,107 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,108 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,108 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2023-09-12T10:54:07,109 /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 2023-09-12T10:54:07,110 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,110 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,111 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,111 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2023-09-12T10:54:07,112 /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 2023-09-12T10:54:07,112 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,113 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,113 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,114 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2023-09-12T10:54:07,114 /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 2023-09-12T10:54:07,115 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,116 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,116 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,117 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2023-09-12T10:54:07,118 /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 2023-09-12T10:54:07,119 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,119 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,120 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,121 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2023-09-12T10:54:07,122 /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 2023-09-12T10:54:07,123 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,123 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,124 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,125 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:806:28: 2023-09-12T10:54:07,125 /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 2023-09-12T10:54:07,126 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,127 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,128 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,128 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:820:28: 2023-09-12T10:54:07,129 /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 2023-09-12T10:54:07,130 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,130 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,131 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,131 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2023-09-12T10:54:07,132 /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 2023-09-12T10:54:07,133 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,133 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:07,134 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGaff; _Alloc = std::allocator]’, 2023-09-12T10:54:07,135 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:1047:45: 2023-09-12T10:54:07,136 /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 2023-09-12T10:54:07,136 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:07,137 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:09,159 /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]’: 2023-09-12T10:54:09,160 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:09,160 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:09,161 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,144 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,145 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, 2023-09-12T10:54:12,145 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1092:34: 2023-09-12T10:54:12,146 /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 2023-09-12T10:54:12,147 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,147 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,148 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,149 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, 2023-09-12T10:54:12,150 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1093:34: 2023-09-12T10:54:12,151 /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 2023-09-12T10:54:12,151 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,152 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,152 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,153 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, 2023-09-12T10:54:12,153 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1105:34: 2023-09-12T10:54:12,154 /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 2023-09-12T10:54:12,154 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,155 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,155 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,156 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, 2023-09-12T10:54:12,157 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1106:34: 2023-09-12T10:54:12,157 /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 2023-09-12T10:54:12,158 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,159 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,160 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,160 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, 2023-09-12T10:54:12,161 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1118:34: 2023-09-12T10:54:12,162 /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 2023-09-12T10:54:12,162 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,163 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,163 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,164 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, 2023-09-12T10:54:12,165 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1119:34: 2023-09-12T10:54:12,166 /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 2023-09-12T10:54:12,167 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,167 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,168 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,168 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, 2023-09-12T10:54:12,169 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1135:34: 2023-09-12T10:54:12,170 /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 2023-09-12T10:54:12,170 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,171 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,171 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,172 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, 2023-09-12T10:54:12,173 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1136:34: 2023-09-12T10:54:12,173 /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 2023-09-12T10:54:12,174 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,175 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,176 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,176 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, 2023-09-12T10:54:12,177 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1137:34: 2023-09-12T10:54:12,178 /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 2023-09-12T10:54:12,179 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,179 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,180 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,181 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, 2023-09-12T10:54:12,181 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1162:34: 2023-09-12T10:54:12,182 /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 2023-09-12T10:54:12,183 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,184 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,184 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,185 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, 2023-09-12T10:54:12,185 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1163:34: 2023-09-12T10:54:12,185 /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 2023-09-12T10:54:12,186 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,186 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,187 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,187 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, 2023-09-12T10:54:12,188 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1164:34: 2023-09-12T10:54:12,188 /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 2023-09-12T10:54:12,189 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,190 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,191 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,191 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, 2023-09-12T10:54:12,192 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1175:34: 2023-09-12T10:54:12,193 /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 2023-09-12T10:54:12,194 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,195 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,195 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,196 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, 2023-09-12T10:54:12,197 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1176:34: 2023-09-12T10:54:12,197 /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 2023-09-12T10:54:12,198 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,199 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,199 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,200 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, 2023-09-12T10:54:12,202 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1194:34: 2023-09-12T10:54:12,202 /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 2023-09-12T10:54:12,202 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,203 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:12,203 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:12,204 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, 2023-09-12T10:54:12,204 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::ParseParamFile()’ at ./src/forcefields/forcefieldgaff.cpp:1195:34: 2023-09-12T10:54:12,205 /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 2023-09-12T10:54:12,205 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:12,206 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:16,480 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:54:16,482 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/cc9Re9Bh.s 2023-09-12T10:54:16,494 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:17,623 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/ 2023-09-12T10:54:17,623 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/ 2023-09-12T10:54:17,624 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/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.' 2023-09-12T10:54:17,628 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 2023-09-12T10:54:17,633 Using built-in specs. 2023-09-12T10:54:17,634 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:17,635 Target: arm-linux-gnueabihf 2023-09-12T10:54:17,635 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 2023-09-12T10:54:17,635 Thread model: posix 2023-09-12T10:54:17,636 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:17,637 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:17,637 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:54:17,638 /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/ccS17LgK.s 2023-09-12T10:54:17,647 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:17,648 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:17,649 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:17,649 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:17,650 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:17,651 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:17,651 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:17,652 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:17,652 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:17,653 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:17,654 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:17,655 #include "..." search starts here: 2023-09-12T10:54:17,655 #include <...> search starts here: 2023-09-12T10:54:17,656 /usr/include/eigen3 2023-09-12T10:54:17,656 include 2023-09-12T10:54:17,657 /usr/include/python3.11 2023-09-12T10:54:17,657 /usr/include/c++/12 2023-09-12T10:54:17,658 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:17,658 /usr/include/c++/12/backward 2023-09-12T10:54:17,658 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:17,659 /usr/local/include 2023-09-12T10:54:17,660 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:17,660 /usr/include 2023-09-12T10:54:17,661 End of search list. 2023-09-12T10:54:17,661 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:17,662 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:17,663 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:17,663 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:17,668 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:19,255 In file included from include/openbabel/atom.h:33, 2023-09-12T10:54:19,256 from include/openbabel/mol.h:43, 2023-09-12T10:54:19,256 from ./src/forcefields/forcefieldghemical.cpp:20: 2023-09-12T10:54:19,257 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:19,258 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:19,258 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:19,259 | ^ 2023-09-12T10:54:19,260 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:19,261 37 | # define UNUSED(x) x 2023-09-12T10:54:19,261 | ^ 2023-09-12T10:54:20,021 In file included from include/openbabel/mol.h:52: 2023-09-12T10:54:20,022 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:20,022 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:20,023 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:20,024 | ^ 2023-09-12T10:54:20,025 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:20,026 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:20,026 | ^~~~~~~~ 2023-09-12T10:54:20,027 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:20,028 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:20,028 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:20,029 | ^ 2023-09-12T10:54:20,030 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:20,031 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:20,031 | ^~~~~~~~ 2023-09-12T10:54:20,047 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:20,047 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:20,048 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:20,049 | ^ 2023-09-12T10:54:20,050 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:20,050 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:20,051 | ^~~~~~~~ 2023-09-12T10:54:20,053 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:20,054 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:20,055 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:20,055 | ^ 2023-09-12T10:54:20,056 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:20,056 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:20,057 | ^~~~~~~~ 2023-09-12T10:54:20,376 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:54:20,377 from include/forcefields/forcefieldghemical.h:23, 2023-09-12T10:54:20,377 from ./src/forcefields/forcefieldghemical.cpp:23: 2023-09-12T10:54:20,378 include/openbabel/plugin.h: At global scope: 2023-09-12T10:54:20,379 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:20,380 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:20,380 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:20,381 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:54:20,382 from /usr/include/c++/12/vector:66, 2023-09-12T10:54:20,383 from include/openbabel/mol.h:35: 2023-09-12T10:54:20,383 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:20,384 131 | struct binary_function 2023-09-12T10:54:20,385 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:20,504 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:54:20,505 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,506 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,506 | ^ 2023-09-12T10:54:20,507 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,508 37 | # define UNUSED(x) x 2023-09-12T10:54:20,509 | ^ 2023-09-12T10:54:20,510 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:54:20,510 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,511 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,512 | ^ 2023-09-12T10:54:20,513 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,513 37 | # define UNUSED(x) x 2023-09-12T10:54:20,514 | ^ 2023-09-12T10:54:20,514 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:54:20,515 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,515 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,516 | ^ 2023-09-12T10:54:20,517 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,517 37 | # define UNUSED(x) x 2023-09-12T10:54:20,518 | ^ 2023-09-12T10:54:20,518 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:54:20,519 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,520 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,520 | ^ 2023-09-12T10:54:20,521 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,521 37 | # define UNUSED(x) x 2023-09-12T10:54:20,522 | ^ 2023-09-12T10:54:20,523 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:54:20,523 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,524 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,525 | ^ 2023-09-12T10:54:20,525 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,526 37 | # define UNUSED(x) x 2023-09-12T10:54:20,527 | ^ 2023-09-12T10:54:20,527 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:54:20,528 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,529 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,530 | ^ 2023-09-12T10:54:20,531 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,531 37 | # define UNUSED(x) x 2023-09-12T10:54:20,532 | ^ 2023-09-12T10:54:20,533 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:54:20,533 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,534 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,535 | ^ 2023-09-12T10:54:20,535 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,536 37 | # define UNUSED(x) x 2023-09-12T10:54:20,537 | ^ 2023-09-12T10:54:20,537 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:54:20,538 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:20,539 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:20,540 | ^ 2023-09-12T10:54:20,540 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:20,541 37 | # define UNUSED(x) x 2023-09-12T10:54:20,542 | ^ 2023-09-12T10:54:28,065 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:54:28,065 /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]’: 2023-09-12T10:54:28,066 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:28,066 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:28,067 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:28,213 /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]’: 2023-09-12T10:54:28,213 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:28,409 /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]’: 2023-09-12T10:54:28,410 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:28,624 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:54:28,624 /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]’: 2023-09-12T10:54:28,625 /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 2023-09-12T10:54:28,626 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:28,627 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:28,728 /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]’: 2023-09-12T10:54:28,728 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:28,729 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:28,730 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:28,878 /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]’: 2023-09-12T10:54:28,879 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:29,564 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,565 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:54:29,566 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, 2023-09-12T10:54:29,566 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, 2023-09-12T10:54:29,567 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, 2023-09-12T10:54:29,567 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:54:29,568 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,568 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,569 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,570 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,570 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,571 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,571 | ^~~~~~~~ 2023-09-12T10:54:29,572 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,572 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:54:29,573 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, 2023-09-12T10:54:29,573 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, 2023-09-12T10:54:29,574 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, 2023-09-12T10:54:29,575 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:54:29,575 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,576 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,577 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,577 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,578 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,579 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,579 | ^~~~~~~~ 2023-09-12T10:54:29,580 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,581 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:54:29,581 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, 2023-09-12T10:54:29,582 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, 2023-09-12T10:54:29,582 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, 2023-09-12T10:54:29,583 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:54:29,584 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,584 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,585 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,585 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,586 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,587 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,587 | ^~~~~~~~ 2023-09-12T10:54:29,588 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:54:29,589 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, 2023-09-12T10:54:29,590 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, 2023-09-12T10:54:29,590 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, 2023-09-12T10:54:29,591 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:54:29,592 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,592 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:54:29,593 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,594 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,594 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,595 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,595 | ^~~~~~~~ 2023-09-12T10:54:29,596 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:54:29,597 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, 2023-09-12T10:54:29,597 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, 2023-09-12T10:54:29,598 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, 2023-09-12T10:54:29,598 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:54:29,599 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,600 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:54:29,600 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,601 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,602 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,602 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,603 | ^~~~~~~~ 2023-09-12T10:54:29,604 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,604 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:54:29,605 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, 2023-09-12T10:54:29,606 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, 2023-09-12T10:54:29,607 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, 2023-09-12T10:54:29,607 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:54:29,608 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,609 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,610 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,611 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,611 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,612 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,613 | ^~~~~~~~ 2023-09-12T10:54:29,613 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,614 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:54:29,614 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, 2023-09-12T10:54:29,615 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, 2023-09-12T10:54:29,616 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, 2023-09-12T10:54:29,616 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:54:29,617 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,618 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,618 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,619 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,620 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,621 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,622 | ^~~~~~~~ 2023-09-12T10:54:29,622 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,623 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2023-09-12T10:54:29,624 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, 2023-09-12T10:54:29,625 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, 2023-09-12T10:54:29,625 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, 2023-09-12T10:54:29,626 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:54:29,627 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,628 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,628 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,629 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,630 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,630 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,631 | ^~~~~~~~ 2023-09-12T10:54:29,632 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:54:29,632 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, 2023-09-12T10:54:29,633 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, 2023-09-12T10:54:29,634 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, 2023-09-12T10:54:29,634 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:54:29,635 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,636 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:54:29,637 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,637 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,638 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,639 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,639 | ^~~~~~~~ 2023-09-12T10:54:29,640 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’, 2023-09-12T10:54:29,641 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, 2023-09-12T10:54:29,642 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, 2023-09-12T10:54:29,642 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, 2023-09-12T10:54:29,643 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:54:29,643 include/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,644 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 2023-09-12T10:54:29,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,645 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,646 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2023-09-12T10:54:29,646 428 | OBFFBondCalculationGhemical bondcalc; 2023-09-12T10:54:29,647 | ^~~~~~~~ 2023-09-12T10:54:29,648 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,648 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,649 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,649 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, 2023-09-12T10:54:29,650 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, 2023-09-12T10:54:29,651 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, 2023-09-12T10:54:29,651 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:54:29,652 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,653 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,653 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,654 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,655 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,656 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,657 | ^~~~~~~~~ 2023-09-12T10:54:29,657 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,658 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,659 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,660 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, 2023-09-12T10:54:29,660 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, 2023-09-12T10:54:29,661 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, 2023-09-12T10:54:29,662 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:54:29,662 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,663 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,663 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,664 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,665 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,665 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,666 | ^~~~~~~~~ 2023-09-12T10:54:29,667 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,667 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,668 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,669 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, 2023-09-12T10:54:29,669 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, 2023-09-12T10:54:29,670 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, 2023-09-12T10:54:29,671 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:54:29,672 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,673 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,674 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,674 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,675 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,676 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,677 | ^~~~~~~~~ 2023-09-12T10:54:29,677 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:29,678 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,678 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, 2023-09-12T10:54:29,679 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, 2023-09-12T10:54:29,680 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, 2023-09-12T10:54:29,680 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:54:29,681 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,682 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:29,682 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,683 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,684 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,685 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,686 | ^~~~~~~~~ 2023-09-12T10:54:29,686 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:54:29,687 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, 2023-09-12T10:54:29,687 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, 2023-09-12T10:54:29,688 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, 2023-09-12T10:54:29,689 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:54:29,690 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,691 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:54:29,691 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,692 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,692 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,693 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,693 | ^~~~~~~~~ 2023-09-12T10:54:29,694 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:54:29,694 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, 2023-09-12T10:54:29,695 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, 2023-09-12T10:54:29,695 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, 2023-09-12T10:54:29,696 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:54:29,697 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,697 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:54:29,698 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,699 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,699 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,700 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,700 | ^~~~~~~~~ 2023-09-12T10:54:29,701 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,702 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,702 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,703 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, 2023-09-12T10:54:29,704 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, 2023-09-12T10:54:29,705 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, 2023-09-12T10:54:29,706 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:54:29,706 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,707 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,708 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,708 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,709 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,709 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,710 | ^~~~~~~~~ 2023-09-12T10:54:29,710 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,711 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,712 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,713 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, 2023-09-12T10:54:29,713 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, 2023-09-12T10:54:29,714 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, 2023-09-12T10:54:29,715 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:54:29,716 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,717 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,717 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,718 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,719 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,720 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,720 | ^~~~~~~~~ 2023-09-12T10:54:29,721 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,722 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,722 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,723 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, 2023-09-12T10:54:29,723 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, 2023-09-12T10:54:29,724 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, 2023-09-12T10:54:29,725 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:54:29,725 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,726 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,726 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,727 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,727 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,728 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,729 | ^~~~~~~~~ 2023-09-12T10:54:29,729 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:29,730 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2023-09-12T10:54:29,730 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, 2023-09-12T10:54:29,731 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, 2023-09-12T10:54:29,732 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, 2023-09-12T10:54:29,732 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:54:29,733 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,734 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:29,735 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,735 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,735 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,736 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,736 | ^~~~~~~~~ 2023-09-12T10:54:29,737 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:54:29,737 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, 2023-09-12T10:54:29,738 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, 2023-09-12T10:54:29,738 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, 2023-09-12T10:54:29,739 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:54:29,739 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,740 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:54:29,741 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,741 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,742 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,742 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,743 | ^~~~~~~~~ 2023-09-12T10:54:29,744 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’, 2023-09-12T10:54:29,745 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, 2023-09-12T10:54:29,745 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, 2023-09-12T10:54:29,746 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, 2023-09-12T10:54:29,747 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:54:29,748 include/forcefields/forcefieldghemical.h:38:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,749 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 2023-09-12T10:54:29,749 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,750 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,750 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2023-09-12T10:54:29,751 494 | OBFFAngleCalculationGhemical anglecalc; 2023-09-12T10:54:29,751 | ^~~~~~~~~ 2023-09-12T10:54:29,752 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,753 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,753 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:29,754 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:54:29,754 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, 2023-09-12T10:54:29,755 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, 2023-09-12T10:54:29,755 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, 2023-09-12T10:54:29,756 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:54:29,757 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,757 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,758 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,759 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,759 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:54:29,760 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:54:29,761 | ^~~~~~~~~~~ 2023-09-12T10:54:29,761 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,762 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,763 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:29,764 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:54:29,765 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, 2023-09-12T10:54:29,766 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, 2023-09-12T10:54:29,766 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, 2023-09-12T10:54:29,767 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:54:29,768 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,768 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,769 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,770 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,771 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:54:29,771 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:54:29,772 | ^~~~~~~~~~~ 2023-09-12T10:54:29,772 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,773 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:54:29,774 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:29,775 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:54:29,776 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, 2023-09-12T10:54:29,776 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, 2023-09-12T10:54:29,777 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, 2023-09-12T10:54:29,778 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:54:29,779 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,780 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,780 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,781 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,781 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:54:29,782 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:54:29,782 | ^~~~~~~~~~~ 2023-09-12T10:54:29,783 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:54:29,783 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:54:29,784 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:54:29,785 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, 2023-09-12T10:54:29,785 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, 2023-09-12T10:54:29,786 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, 2023-09-12T10:54:29,787 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:54:29,787 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,788 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:54:29,789 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,790 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,790 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:54:29,791 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:54:29,792 | ^~~~~~~~~~~ 2023-09-12T10:54:29,793 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:54:29,793 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2023-09-12T10:54:29,794 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, 2023-09-12T10:54:29,795 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, 2023-09-12T10:54:29,796 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, 2023-09-12T10:54:29,796 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:54:29,797 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,798 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:54:29,798 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,799 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,800 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:54:29,800 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:54:29,801 | ^~~~~~~~~~~ 2023-09-12T10:54:29,801 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’, 2023-09-12T10:54:29,802 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, 2023-09-12T10:54:29,803 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, 2023-09-12T10:54:29,804 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, 2023-09-12T10:54:29,805 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:54:29,805 include/forcefields/forcefieldghemical.h:46:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,806 46 | class OBFFTorsionCalculationGhemical : public OBFFCalculation4 2023-09-12T10:54:29,807 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,808 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,808 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2023-09-12T10:54:29,809 560 | OBFFTorsionCalculationGhemical torsioncalc; 2023-09-12T10:54:29,810 | ^~~~~~~~~~~ 2023-09-12T10:54:29,811 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,812 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2023-09-12T10:54:29,812 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, 2023-09-12T10:54:29,813 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, 2023-09-12T10:54:29,814 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, 2023-09-12T10:54:29,815 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:54:29,815 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,816 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,816 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,817 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,817 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:54:29,818 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:54:29,818 | ^~~~~~~ 2023-09-12T10:54:29,819 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,820 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2023-09-12T10:54:29,820 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, 2023-09-12T10:54:29,821 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, 2023-09-12T10:54:29,822 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, 2023-09-12T10:54:29,822 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:54:29,823 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,824 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,824 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,825 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,826 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:54:29,826 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:54:29,827 | ^~~~~~~ 2023-09-12T10:54:29,828 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,828 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2023-09-12T10:54:29,829 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, 2023-09-12T10:54:29,829 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, 2023-09-12T10:54:29,830 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, 2023-09-12T10:54:29,830 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:54:29,831 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,831 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,832 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,832 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,833 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:54:29,833 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:54:29,834 | ^~~~~~~ 2023-09-12T10:54:29,834 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2023-09-12T10:54:29,835 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, 2023-09-12T10:54:29,836 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, 2023-09-12T10:54:29,836 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, 2023-09-12T10:54:29,837 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:54:29,837 include/forcefields/forcefieldghemical.h:56:9: warning: ‘vdwcalc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,838 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2023-09-12T10:54:29,839 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,839 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,840 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:54:29,841 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:54:29,841 | ^~~~~~~ 2023-09-12T10:54:29,842 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2023-09-12T10:54:29,842 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, 2023-09-12T10:54:29,843 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, 2023-09-12T10:54:29,843 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, 2023-09-12T10:54:29,844 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:54:29,844 include/forcefields/forcefieldghemical.h:56:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,845 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2023-09-12T10:54:29,845 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,846 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,847 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2023-09-12T10:54:29,847 676 | OBFFVDWCalculationGhemical vdwcalc; 2023-09-12T10:54:29,848 | ^~~~~~~ 2023-09-12T10:54:29,848 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,849 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2023-09-12T10:54:29,850 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, 2023-09-12T10:54:29,851 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, 2023-09-12T10:54:29,851 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, 2023-09-12T10:54:29,852 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:54:29,853 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,853 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,854 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,855 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,855 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2023-09-12T10:54:29,856 780 | OBFFElectrostaticCalculationGhemical elecalc; 2023-09-12T10:54:29,856 | ^~~~~~~ 2023-09-12T10:54:29,857 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,857 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2023-09-12T10:54:29,858 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, 2023-09-12T10:54:29,858 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, 2023-09-12T10:54:29,859 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, 2023-09-12T10:54:29,859 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:54:29,860 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,860 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,861 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,862 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,862 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2023-09-12T10:54:29,863 780 | OBFFElectrostaticCalculationGhemical elecalc; 2023-09-12T10:54:29,863 | ^~~~~~~ 2023-09-12T10:54:29,864 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:54:29,865 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2023-09-12T10:54:29,865 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, 2023-09-12T10:54:29,866 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, 2023-09-12T10:54:29,866 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, 2023-09-12T10:54:29,867 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:54:29,868 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:29,868 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:54:29,869 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:54:29,869 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2023-09-12T10:54:29,870 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2023-09-12T10:54:29,870 780 | OBFFElectrostaticCalculationGhemical elecalc; 2023-09-12T10:54:29,871 | ^~~~~~~ 2023-09-12T10:54:29,871 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:54:29,872 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2023-09-12T10:54:29,872 /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 2023-09-12T10:54:29,873 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:29,874 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:29,874 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:54:29,875 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2023-09-12T10:54:29,875 /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 2023-09-12T10:54:29,876 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:29,877 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:29,877 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:54:29,878 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2023-09-12T10:54:29,878 /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 2023-09-12T10:54:29,879 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:29,879 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:29,880 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:54:29,881 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2023-09-12T10:54:29,881 /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 2023-09-12T10:54:29,882 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:29,882 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:29,883 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:54:29,883 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2023-09-12T10:54:29,884 /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 2023-09-12T10:54:29,884 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:29,885 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:29,885 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:54:29,886 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2023-09-12T10:54:29,886 /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 2023-09-12T10:54:29,887 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:29,887 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:29,888 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’, 2023-09-12T10:54:29,889 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2023-09-12T10:54:29,889 /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 2023-09-12T10:54:29,890 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:54:29,890 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:54:31,408 /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]’: 2023-09-12T10:54:31,408 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:31,409 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:31,410 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,887 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:33,888 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, 2023-09-12T10:54:33,890 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:870:34: 2023-09-12T10:54:33,890 /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 2023-09-12T10:54:33,891 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:33,892 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,893 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:33,893 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, 2023-09-12T10:54:33,894 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:871:34: 2023-09-12T10:54:33,894 /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 2023-09-12T10:54:33,895 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:33,896 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,896 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:33,897 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, 2023-09-12T10:54:33,897 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:888:34: 2023-09-12T10:54:33,898 /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 2023-09-12T10:54:33,899 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:33,899 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,900 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:33,901 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, 2023-09-12T10:54:33,902 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:889:34: 2023-09-12T10:54:33,903 /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 2023-09-12T10:54:33,903 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:33,904 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,905 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:33,906 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, 2023-09-12T10:54:33,906 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:920:34: 2023-09-12T10:54:33,907 /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 2023-09-12T10:54:33,908 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:33,908 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,909 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:33,910 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, 2023-09-12T10:54:33,911 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:921:34: 2023-09-12T10:54:33,911 /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 2023-09-12T10:54:33,912 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:33,912 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:33,913 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:33,914 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, 2023-09-12T10:54:33,914 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::ParseParamFile()’ at ./src/forcefields/forcefieldghemical.cpp:933:34: 2023-09-12T10:54:33,915 /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 2023-09-12T10:54:33,915 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:33,916 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:36,644 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:54:36,645 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/ccS17LgK.s 2023-09-12T10:54:36,649 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:37,699 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/ 2023-09-12T10:54:37,700 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/ 2023-09-12T10:54:37,700 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:54:37,705 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 2023-09-12T10:54:37,709 Using built-in specs. 2023-09-12T10:54:37,710 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:37,711 Target: arm-linux-gnueabihf 2023-09-12T10:54:37,711 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 2023-09-12T10:54:37,711 Thread model: posix 2023-09-12T10:54:37,712 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:37,713 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:37,713 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:54:37,714 /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/cccRlCEd.s 2023-09-12T10:54:37,724 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:37,724 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:37,725 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:37,726 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:37,727 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:37,728 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:37,728 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:37,729 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:37,730 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:37,731 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:37,732 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:37,734 #include "..." search starts here: 2023-09-12T10:54:37,735 #include <...> search starts here: 2023-09-12T10:54:37,735 /usr/include/eigen3 2023-09-12T10:54:37,736 include 2023-09-12T10:54:37,736 /usr/include/python3.11 2023-09-12T10:54:37,737 /usr/include/c++/12 2023-09-12T10:54:37,737 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:37,738 /usr/include/c++/12/backward 2023-09-12T10:54:37,738 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:37,738 /usr/local/include 2023-09-12T10:54:37,739 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:37,739 /usr/include 2023-09-12T10:54:37,740 End of search list. 2023-09-12T10:54:37,740 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:37,741 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:37,742 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:37,742 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:37,743 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:38,079 In file included from ./src/forcefields/forcefieldmm2.cpp:21: 2023-09-12T10:54:38,080 include/forcefields/forcefieldmm2.h:68:57: warning: multi-line comment [-Wcomment] 2023-09-12T10:54:38,080 68 | // b = atom d \ 2023-09-12T10:54:38,081 | ^ 2023-09-12T10:54:38,082 ./src/forcefields/forcefieldmm2.cpp:276:3: warning: multi-line comment [-Wcomment] 2023-09-12T10:54:38,082 276 | // \ 2023-09-12T10:54:38,083 | ^ 2023-09-12T10:54:39,302 In file included from include/openbabel/atom.h:33, 2023-09-12T10:54:39,303 from include/openbabel/mol.h:43, 2023-09-12T10:54:39,303 from ./src/forcefields/forcefieldmm2.cpp:19: 2023-09-12T10:54:39,304 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:39,305 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:39,306 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:39,307 | ^ 2023-09-12T10:54:39,307 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:39,308 37 | # define UNUSED(x) x 2023-09-12T10:54:39,309 | ^ 2023-09-12T10:54:40,068 In file included from include/openbabel/mol.h:52: 2023-09-12T10:54:40,069 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,070 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,071 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:40,071 | ^ 2023-09-12T10:54:40,072 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:40,073 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:40,074 | ^~~~~~~~ 2023-09-12T10:54:40,075 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,076 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,076 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:40,078 | ^ 2023-09-12T10:54:40,078 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:40,079 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:40,079 | ^~~~~~~~ 2023-09-12T10:54:40,093 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,093 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,094 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:40,094 | ^ 2023-09-12T10:54:40,095 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:40,096 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:40,096 | ^~~~~~~~ 2023-09-12T10:54:40,099 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:40,100 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,100 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:40,101 | ^ 2023-09-12T10:54:40,102 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:40,103 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:40,104 | ^~~~~~~~ 2023-09-12T10:54:40,411 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:54:40,411 from include/forcefields/forcefieldmm2.h:23: 2023-09-12T10:54:40,412 include/openbabel/plugin.h: At global scope: 2023-09-12T10:54:40,413 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:40,414 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:40,414 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:40,415 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:54:40,416 from /usr/include/c++/12/vector:66, 2023-09-12T10:54:40,416 from include/openbabel/mol.h:35: 2023-09-12T10:54:40,417 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:40,418 131 | struct binary_function 2023-09-12T10:54:40,418 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:40,538 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:54:40,539 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,540 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,541 | ^ 2023-09-12T10:54:40,542 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,542 37 | # define UNUSED(x) x 2023-09-12T10:54:40,543 | ^ 2023-09-12T10:54:40,543 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:54:40,544 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,544 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,545 | ^ 2023-09-12T10:54:40,546 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,546 37 | # define UNUSED(x) x 2023-09-12T10:54:40,547 | ^ 2023-09-12T10:54:40,547 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:54:40,548 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,548 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,549 | ^ 2023-09-12T10:54:40,550 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,550 37 | # define UNUSED(x) x 2023-09-12T10:54:40,551 | ^ 2023-09-12T10:54:40,551 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:54:40,552 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,553 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,553 | ^ 2023-09-12T10:54:40,554 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,555 37 | # define UNUSED(x) x 2023-09-12T10:54:40,556 | ^ 2023-09-12T10:54:40,556 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:54:40,557 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,558 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,559 | ^ 2023-09-12T10:54:40,559 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,560 37 | # define UNUSED(x) x 2023-09-12T10:54:40,561 | ^ 2023-09-12T10:54:40,561 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:54:40,562 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,563 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,563 | ^ 2023-09-12T10:54:40,564 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,565 37 | # define UNUSED(x) x 2023-09-12T10:54:40,565 | ^ 2023-09-12T10:54:40,566 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:54:40,567 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,567 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,568 | ^ 2023-09-12T10:54:40,569 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,570 37 | # define UNUSED(x) x 2023-09-12T10:54:40,571 | ^ 2023-09-12T10:54:40,571 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:54:40,572 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:40,572 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:40,572 | ^ 2023-09-12T10:54:40,573 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:40,573 37 | # define UNUSED(x) x 2023-09-12T10:54:40,574 | ^ 2023-09-12T10:54:40,584 include/forcefields/forcefieldmm2.h: In member function ‘virtual OpenBabel::OBForceFieldMM2* OpenBabel::OBForceFieldMM2::MakeNewInstance()’: 2023-09-12T10:54:40,585 include/forcefields/forcefieldmm2.h:97:83: warning: implicitly-declared ‘OpenBabel::OBForceFieldMM2::OBForceFieldMM2(const OpenBabel::OBForceFieldMM2&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:40,585 97 | virtual OBForceFieldMM2* MakeNewInstance(){ return new OBForceFieldMM2(*this); } 2023-09-12T10:54:40,586 | ^ 2023-09-12T10:54:40,587 include/forcefields/forcefieldmm2.h:107:24: note: because ‘OpenBabel::OBForceFieldMM2’ has user-provided ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’ 2023-09-12T10:54:40,587 107 | OBForceFieldMM2 &operator = (OBForceFieldMM2 &); 2023-09-12T10:54:40,588 | ^~~~~~~~ 2023-09-12T10:54:40,600 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_Angle()’: 2023-09-12T10:54:40,600 ./src/forcefields/forcefieldmm2.cpp:81:59: warning: variable ‘delta3’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:54:40,601 81 | double e, energy, force, ang, ang_ref, delta, delta2, delta3, delta4, f, dotprod, rab, rab2, rab3, rbc, rbc2, rbc3, root, dotprod_abbc; 2023-09-12T10:54:40,602 | ^~~~~~ 2023-09-12T10:54:40,615 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_OOP()’: 2023-09-12T10:54:40,615 ./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] 2023-09-12T10:54:40,616 292 | for (int idx=0; idx < _ffoutplanebendparams.size(); idx++) { 2023-09-12T10:54:40,617 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:42,013 ./src/forcefields/forcefieldmm2.cpp: In member function ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’: 2023-09-12T10:54:42,014 ./src/forcefields/forcefieldmm2.cpp:503:3: warning: control reaches end of non-void function [-Wreturn-type] 2023-09-12T10:54:42,014 503 | } 2023-09-12T10:54:42,015 | ^ 2023-09-12T10:54:45,580 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:54:45,580 /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]’: 2023-09-12T10:54:45,581 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:54:45,582 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:54:45,583 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,118 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,119 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, 2023-09-12T10:54:46,120 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:600:34: 2023-09-12T10:54:46,121 /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 2023-09-12T10:54:46,121 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,122 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,122 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,123 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, 2023-09-12T10:54:46,124 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:601:34: 2023-09-12T10:54:46,124 /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 2023-09-12T10:54:46,125 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,125 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,126 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,127 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, 2023-09-12T10:54:46,127 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:614:34: 2023-09-12T10:54:46,128 /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 2023-09-12T10:54:46,129 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,129 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,130 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,131 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, 2023-09-12T10:54:46,132 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:615:34: 2023-09-12T10:54:46,132 /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 2023-09-12T10:54:46,133 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,134 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,135 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,135 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, 2023-09-12T10:54:46,136 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:621:34: 2023-09-12T10:54:46,137 /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 2023-09-12T10:54:46,138 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,139 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,139 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,140 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, 2023-09-12T10:54:46,141 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:632:34: 2023-09-12T10:54:46,141 /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 2023-09-12T10:54:46,142 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,142 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,143 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,144 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, 2023-09-12T10:54:46,144 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:633:34: 2023-09-12T10:54:46,145 /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 2023-09-12T10:54:46,146 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,146 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,147 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,148 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, 2023-09-12T10:54:46,148 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:634:34: 2023-09-12T10:54:46,149 /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 2023-09-12T10:54:46,150 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,150 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,151 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,152 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, 2023-09-12T10:54:46,153 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:641:34: 2023-09-12T10:54:46,153 /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 2023-09-12T10:54:46,154 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,156 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,156 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,157 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, 2023-09-12T10:54:46,157 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:648:34: 2023-09-12T10:54:46,158 /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 2023-09-12T10:54:46,158 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,159 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,160 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,160 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, 2023-09-12T10:54:46,161 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:649:34: 2023-09-12T10:54:46,161 /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 2023-09-12T10:54:46,162 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,162 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,163 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,164 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, 2023-09-12T10:54:46,164 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:655:34: 2023-09-12T10:54:46,165 /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 2023-09-12T10:54:46,166 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,166 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,167 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,168 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, 2023-09-12T10:54:46,168 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:656:34: 2023-09-12T10:54:46,169 /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 2023-09-12T10:54:46,169 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,170 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,171 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,172 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, 2023-09-12T10:54:46,172 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:663:34: 2023-09-12T10:54:46,173 /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 2023-09-12T10:54:46,174 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,174 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:46,175 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:54:46,175 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, 2023-09-12T10:54:46,176 inlined from ‘virtual bool OpenBabel::OBForceFieldMM2::ParseParamFile()’ at ./src/forcefields/forcefieldmm2.cpp:664:34: 2023-09-12T10:54:46,177 /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 2023-09-12T10:54:46,177 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:54:46,178 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:48,566 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/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/' 2023-09-12T10:54:48,567 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/cccRlCEd.s 2023-09-12T10:54:48,572 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:54:49,277 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/ 2023-09-12T10:54:49,278 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/ 2023-09-12T10:54:49,278 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2023-09-12T10:54:49,283 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 2023-09-12T10:54:49,287 Using built-in specs. 2023-09-12T10:54:49,288 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:54:49,288 Target: arm-linux-gnueabihf 2023-09-12T10:54:49,289 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 2023-09-12T10:54:49,289 Thread model: posix 2023-09-12T10:54:49,290 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:54:49,290 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:54:49,291 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/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/' 2023-09-12T10:54:49,291 /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/ccjrpli3.s 2023-09-12T10:54:49,300 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:49,301 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:49,301 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:49,302 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:49,303 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:54:49,303 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:54:49,304 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:54:49,304 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:54:49,305 ignoring duplicate directory "/usr/include/" 2023-09-12T10:54:49,306 as it is a non-system directory that duplicates a system directory 2023-09-12T10:54:49,306 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:54:49,307 #include "..." search starts here: 2023-09-12T10:54:49,308 #include <...> search starts here: 2023-09-12T10:54:49,308 /usr/include/eigen3 2023-09-12T10:54:49,309 include 2023-09-12T10:54:49,309 /usr/include/python3.11 2023-09-12T10:54:49,310 /usr/include/c++/12 2023-09-12T10:54:49,310 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:54:49,311 /usr/include/c++/12/backward 2023-09-12T10:54:49,311 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:54:49,311 /usr/local/include 2023-09-12T10:54:49,312 /usr/include/arm-linux-gnueabihf 2023-09-12T10:54:49,312 /usr/include 2023-09-12T10:54:49,313 End of search list. 2023-09-12T10:54:49,313 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:54:49,314 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:54:49,315 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:54:49,315 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:54:49,321 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:54:50,892 In file included from include/openbabel/format.h:22, 2023-09-12T10:54:50,893 from include/openbabel/obconversion.h:37, 2023-09-12T10:54:50,893 from ./src/forcefields/forcefieldmmff94.cpp:31: 2023-09-12T10:54:50,894 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:54:50,894 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:54:50,895 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:50,896 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:54:50,896 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:54:50,897 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:54:50,898 from /usr/include/c++/12/ios:42, 2023-09-12T10:54:50,898 from /usr/include/c++/12/ostream:38, 2023-09-12T10:54:50,899 from /usr/include/c++/12/iostream:39, 2023-09-12T10:54:50,900 from include/openbabel/obconversion.h:24: 2023-09-12T10:54:50,901 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:54:50,901 131 | struct binary_function 2023-09-12T10:54:50,902 | ^~~~~~~~~~~~~~~ 2023-09-12T10:54:51,119 In file included from include/openbabel/atom.h:33, 2023-09-12T10:54:51,120 from include/openbabel/mol.h:43, 2023-09-12T10:54:51,121 from ./src/forcefields/forcefieldmmff94.cpp:32: 2023-09-12T10:54:51,122 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:54:51,122 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:54:51,123 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:54:51,124 | ^ 2023-09-12T10:54:51,124 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:51,125 37 | # define UNUSED(x) x 2023-09-12T10:54:51,126 | ^ 2023-09-12T10:54:51,790 In file included from include/openbabel/mol.h:52: 2023-09-12T10:54:51,791 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:51,791 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:51,792 862 | {return new OBVibrationData(*this);} 2023-09-12T10:54:51,793 | ^ 2023-09-12T10:54:51,794 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:54:51,795 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:54:51,795 | ^~~~~~~~ 2023-09-12T10:54:51,796 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:51,796 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:51,797 907 | {return new OBDOSData(*this);} 2023-09-12T10:54:51,797 | ^ 2023-09-12T10:54:51,798 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:54:51,799 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:54:51,799 | ^~~~~~~~ 2023-09-12T10:54:51,817 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:51,818 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:51,819 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:54:51,819 | ^ 2023-09-12T10:54:51,820 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:54:51,821 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:54:51,821 | ^~~~~~~~ 2023-09-12T10:54:51,825 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:54:51,826 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:54:51,826 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:54:51,827 | ^ 2023-09-12T10:54:51,828 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:54:51,829 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:54:51,829 | ^~~~~~~~ 2023-09-12T10:54:52,249 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:54:52,250 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,250 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,251 | ^ 2023-09-12T10:54:52,252 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,253 37 | # define UNUSED(x) x 2023-09-12T10:54:52,253 | ^ 2023-09-12T10:54:52,254 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:54:52,255 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,256 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,256 | ^ 2023-09-12T10:54:52,257 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,257 37 | # define UNUSED(x) x 2023-09-12T10:54:52,258 | ^ 2023-09-12T10:54:52,258 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:54:52,259 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,260 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,260 | ^ 2023-09-12T10:54:52,261 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,261 37 | # define UNUSED(x) x 2023-09-12T10:54:52,262 | ^ 2023-09-12T10:54:52,263 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:54:52,263 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,264 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,264 | ^ 2023-09-12T10:54:52,265 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,266 37 | # define UNUSED(x) x 2023-09-12T10:54:52,266 | ^ 2023-09-12T10:54:52,267 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:54:52,268 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,268 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,269 | ^ 2023-09-12T10:54:52,270 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,271 37 | # define UNUSED(x) x 2023-09-12T10:54:52,271 | ^ 2023-09-12T10:54:52,272 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:54:52,273 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,274 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,274 | ^ 2023-09-12T10:54:52,275 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,275 37 | # define UNUSED(x) x 2023-09-12T10:54:52,276 | ^ 2023-09-12T10:54:52,277 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:54:52,277 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,278 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,279 | ^ 2023-09-12T10:54:52,279 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,280 37 | # define UNUSED(x) x 2023-09-12T10:54:52,280 | ^ 2023-09-12T10:54:52,281 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:54:52,282 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:54:52,283 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:54:52,284 | ^ 2023-09-12T10:54:52,284 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:54:52,285 37 | # define UNUSED(x) x 2023-09-12T10:54:52,285 | ^ 2023-09-12T10:54:52,577 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:54:52,578 ./src/forcefields/forcefieldmmff94.cpp:2790:32: warning: variable ‘bondtype1’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:54:52,578 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2023-09-12T10:54:52,578 | ^~~~~~~~~ 2023-09-12T10:54:52,579 ./src/forcefields/forcefieldmmff94.cpp:2790:43: warning: variable ‘bondtype2’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:54:52,580 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2023-09-12T10:54:52,580 | ^~~~~~~~~ 2023-09-12T10:54:53,048 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = true]’: 2023-09-12T10:54:53,048 include/forcefields/forcefieldmmff94.h:288:40: required from here 2023-09-12T10:54:53,049 ./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] 2023-09-12T10:54:53,050 140 | for (int i = 0; i < _bondcalculations.size(); ++i) { 2023-09-12T10:54:53,050 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:53,051 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = false]’: 2023-09-12T10:54:53,051 include/forcefields/forcefieldmmff94.h:288:58: required from here 2023-09-12T10:54:53,052 ./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] 2023-09-12T10:54:53,053 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = true]’: 2023-09-12T10:54:53,054 include/forcefields/forcefieldmmff94.h:294:41: required from here 2023-09-12T10:54:53,055 ./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] 2023-09-12T10:54:53,055 255 | for (int i = 0; i < _anglecalculations.size(); ++i) { 2023-09-12T10:54:53,056 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:53,057 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = false]’: 2023-09-12T10:54:53,058 include/forcefields/forcefieldmmff94.h:294:60: required from here 2023-09-12T10:54:53,058 ./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] 2023-09-12T10:54:53,059 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = true]’: 2023-09-12T10:54:53,060 include/forcefields/forcefieldmmff94.h:300:42: required from here 2023-09-12T10:54:53,061 ./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] 2023-09-12T10:54:53,061 368 | for (int i = 0; i < _strbndcalculations.size(); ++i) { 2023-09-12T10:54:53,062 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:53,063 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = false]’: 2023-09-12T10:54:53,064 include/forcefields/forcefieldmmff94.h:300:62: required from here 2023-09-12T10:54:53,064 ./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] 2023-09-12T10:54:53,065 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = true]’: 2023-09-12T10:54:53,066 include/forcefields/forcefieldmmff94.h:306:43: required from here 2023-09-12T10:54:53,067 ./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] 2023-09-12T10:54:53,067 504 | for (int i = 0; i < _torsioncalculations.size(); ++i) { 2023-09-12T10:54:53,068 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:53,069 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = false]’: 2023-09-12T10:54:53,069 include/forcefields/forcefieldmmff94.h:306:64: required from here 2023-09-12T10:54:53,070 ./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] 2023-09-12T10:54:53,072 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = true]’: 2023-09-12T10:54:53,073 include/forcefields/forcefieldmmff94.h:312:39: required from here 2023-09-12T10:54:53,073 ./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] 2023-09-12T10:54:53,074 602 | for (int i = 0; i < _oopcalculations.size(); ++i) { 2023-09-12T10:54:53,075 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:53,076 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = false]’: 2023-09-12T10:54:53,076 include/forcefields/forcefieldmmff94.h:312:56: required from here 2023-09-12T10:54:53,077 ./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] 2023-09-12T10:54:53,078 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = true]’: 2023-09-12T10:54:53,079 include/forcefields/forcefieldmmff94.h:318:39: required from here 2023-09-12T10:54:53,080 ./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] 2023-09-12T10:54:53,080 699 | for (int i = 0; i < _vdwcalculations.size(); ++i) { 2023-09-12T10:54:53,081 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:53,082 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = false]’: 2023-09-12T10:54:53,082 include/forcefields/forcefieldmmff94.h:318:56: required from here 2023-09-12T10:54:53,083 ./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] 2023-09-12T10:54:53,084 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = true]’: 2023-09-12T10:54:53,085 include/forcefields/forcefieldmmff94.h:324:49: required from here 2023-09-12T10:54:53,085 ./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] 2023-09-12T10:54:53,086 785 | for (int i = 0; i < _electrostaticcalculations.size(); ++i) { 2023-09-12T10:54:53,086 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:54:53,087 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = false]’: 2023-09-12T10:54:53,087 include/forcefields/forcefieldmmff94.h:324:76: required from here 2023-09-12T10:54:53,088 ./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] 2023-09-12T10:54:54,601 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘int OpenBabel::OBForceFieldMMFF94::GetStrBndType(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*)’: 2023-09-12T10:54:54,602 ./src/forcefields/forcefieldmmff94.cpp:4540:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:54:54,602 4540 | if (btbc) { 2023-09-12T10:54:54,603 | ^~ 2023-09-12T10:54:54,604 ./src/forcefields/forcefieldmmff94.cpp:4548:5: note: here 2023-09-12T10:54:54,605 4548 | case 2: 2023-09-12T10:54:54,605 | ^~~~ 2023-09-12T10:54:54,606 ./src/forcefields/forcefieldmmff94.cpp:4565:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:54:54,607 4565 | if (btbc) { 2023-09-12T10:54:54,607 | ^~ 2023-09-12T10:54:54,608 ./src/forcefields/forcefieldmmff94.cpp:4573:5: note: here 2023-09-12T10:54:54,609 4573 | case 6: 2023-09-12T10:54:54,610 | ^~~~ 2023-09-12T10:54:54,610 ./src/forcefields/forcefieldmmff94.cpp:4584:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:54:54,611 4584 | if (btbc) { 2023-09-12T10:54:54,612 | ^~ 2023-09-12T10:54:54,612 ./src/forcefields/forcefieldmmff94.cpp:4592:5: note: here 2023-09-12T10:54:54,613 4592 | case 8: 2023-09-12T10:54:54,613 | ^~~~ 2023-09-12T10:54:58,868 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘bool OpenBabel::OBForceFieldMMFF94::PerceiveAromatic()’: 2023-09-12T10:54:58,868 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘first_rj’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:58,869 1443 | ringbond = _mol.GetBond(first_rj, index); 2023-09-12T10:54:58,869 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:54:58,870 ./src/forcefields/forcefieldmmff94.cpp:1380:29: note: ‘first_rj’ was declared here 2023-09-12T10:54:58,871 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2023-09-12T10:54:58,871 | ^~~~~~~~ 2023-09-12T10:54:58,872 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:54:58,873 1443 | ringbond = _mol.GetBond(first_rj, index); 2023-09-12T10:54:58,874 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:54:58,875 ./src/forcefields/forcefieldmmff94.cpp:1380:12: note: ‘index’ was declared here 2023-09-12T10:54:58,875 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2023-09-12T10:54:58,875 | ^~~~~ 2023-09-12T10:55:02,017 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:55:02,018 from include/openbabel/obconversion.h:30: 2023-09-12T10:55:02,019 /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]’: 2023-09-12T10:55:02,019 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:02,020 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:55:02,020 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:02,167 /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]’: 2023-09-12T10:55:02,168 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:02,378 /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]’: 2023-09-12T10:55:02,378 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:03,159 /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]’: 2023-09-12T10:55:03,160 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:03,402 /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]’: 2023-09-12T10:55:03,403 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:03,581 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:55:03,582 /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]’: 2023-09-12T10:55:03,583 /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 2023-09-12T10:55:03,583 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:03,584 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:03,684 /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]’: 2023-09-12T10:55:03,685 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:03,685 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:55:03,686 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:03,865 /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]’: 2023-09-12T10:55:03,866 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:04,810 In file included from include/forcefields/forcefieldmmff94.h:24, 2023-09-12T10:55:04,811 from ./src/forcefields/forcefieldmmff94.cpp:36: 2023-09-12T10:55:04,819 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,820 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:55:04,820 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, 2023-09-12T10:55:04,821 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, 2023-09-12T10:55:04,822 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, 2023-09-12T10:55:04,823 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:55:04,823 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,824 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,825 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,825 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,826 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,827 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,827 | ^~~~~~~~ 2023-09-12T10:55:04,828 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,829 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:55:04,829 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, 2023-09-12T10:55:04,830 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, 2023-09-12T10:55:04,831 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, 2023-09-12T10:55:04,831 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:55:04,831 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,832 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,832 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,833 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,833 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,833 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,834 | ^~~~~~~~ 2023-09-12T10:55:04,834 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,835 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:55:04,836 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, 2023-09-12T10:55:04,836 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, 2023-09-12T10:55:04,837 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, 2023-09-12T10:55:04,837 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:55:04,838 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,838 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,839 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,839 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,840 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,840 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,841 | ^~~~~~~~ 2023-09-12T10:55:04,842 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:55:04,842 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, 2023-09-12T10:55:04,843 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, 2023-09-12T10:55:04,844 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, 2023-09-12T10:55:04,844 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:55:04,845 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,845 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:55:04,845 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,846 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,846 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,847 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,847 | ^~~~~~~~ 2023-09-12T10:55:04,847 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:55:04,848 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, 2023-09-12T10:55:04,849 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, 2023-09-12T10:55:04,849 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, 2023-09-12T10:55:04,850 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:55:04,850 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,851 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:55:04,851 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,852 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,852 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,853 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,853 | ^~~~~~~~ 2023-09-12T10:55:04,854 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,855 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:55:04,855 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, 2023-09-12T10:55:04,856 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, 2023-09-12T10:55:04,856 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, 2023-09-12T10:55:04,857 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:55:04,857 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,857 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,858 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,858 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,859 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,859 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,860 | ^~~~~~~~ 2023-09-12T10:55:04,861 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,861 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:55:04,862 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, 2023-09-12T10:55:04,862 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, 2023-09-12T10:55:04,863 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, 2023-09-12T10:55:04,864 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:55:04,864 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,865 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,865 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,866 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,866 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,867 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,868 | ^~~~~~~~ 2023-09-12T10:55:04,868 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,868 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2023-09-12T10:55:04,869 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, 2023-09-12T10:55:04,869 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, 2023-09-12T10:55:04,870 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, 2023-09-12T10:55:04,870 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:55:04,871 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,871 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,872 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,873 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,874 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,874 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,875 | ^~~~~~~~ 2023-09-12T10:55:04,875 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:55:04,876 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, 2023-09-12T10:55:04,877 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, 2023-09-12T10:55:04,877 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, 2023-09-12T10:55:04,878 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:55:04,878 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,879 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:55:04,879 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,880 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,881 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,881 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,882 | ^~~~~~~~ 2023-09-12T10:55:04,882 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’, 2023-09-12T10:55:04,883 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, 2023-09-12T10:55:04,883 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, 2023-09-12T10:55:04,884 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, 2023-09-12T10:55:04,884 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:55:04,884 include/forcefields/forcefieldmmff94.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,885 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 2023-09-12T10:55:04,885 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,886 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,886 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2023-09-12T10:55:04,887 2699 | OBFFBondCalculationMMFF94 bondcalc; 2023-09-12T10:55:04,887 | ^~~~~~~~ 2023-09-12T10:55:04,888 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,888 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:04,889 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:55:04,890 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, 2023-09-12T10:55:04,890 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, 2023-09-12T10:55:04,891 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, 2023-09-12T10:55:04,891 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:55:04,892 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,893 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,893 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,894 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,894 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:55:04,895 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:55:04,895 | ^~~~~~~~~ 2023-09-12T10:55:04,895 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,896 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:04,896 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:55:04,897 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, 2023-09-12T10:55:04,897 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, 2023-09-12T10:55:04,897 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, 2023-09-12T10:55:04,898 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:55:04,899 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,899 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,900 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,901 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,901 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:55:04,902 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:55:04,902 | ^~~~~~~~~ 2023-09-12T10:55:04,903 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,903 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:04,904 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:55:04,904 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, 2023-09-12T10:55:04,905 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, 2023-09-12T10:55:04,906 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, 2023-09-12T10:55:04,906 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:55:04,907 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,907 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,907 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,908 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,908 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:55:04,909 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:55:04,909 | ^~~~~~~~~ 2023-09-12T10:55:04,909 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:55:04,910 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2023-09-12T10:55:04,910 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, 2023-09-12T10:55:04,911 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, 2023-09-12T10:55:04,911 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, 2023-09-12T10:55:04,912 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:55:04,913 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,913 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:55:04,914 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,914 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,915 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:55:04,915 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:55:04,916 | ^~~~~~~~~ 2023-09-12T10:55:04,916 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2023-09-12T10:55:04,917 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, 2023-09-12T10:55:04,918 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, 2023-09-12T10:55:04,918 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, 2023-09-12T10:55:04,918 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:55:04,919 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,920 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:04,920 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,920 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,921 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:55:04,921 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:55:04,922 | ^~~~~~~~~ 2023-09-12T10:55:04,922 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2023-09-12T10:55:04,923 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, 2023-09-12T10:55:04,923 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, 2023-09-12T10:55:04,924 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, 2023-09-12T10:55:04,925 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:55:04,925 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,926 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:04,926 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,927 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,927 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2023-09-12T10:55:04,928 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2023-09-12T10:55:04,928 | ^~~~~~~~~ 2023-09-12T10:55:04,929 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,930 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:04,930 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:55:04,931 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, 2023-09-12T10:55:04,932 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, 2023-09-12T10:55:04,933 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, 2023-09-12T10:55:04,933 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:04,934 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,935 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,935 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,936 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,937 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:04,937 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:04,938 | ^~~~~~~~~~ 2023-09-12T10:55:04,939 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,940 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:04,940 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:55:04,941 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, 2023-09-12T10:55:04,942 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, 2023-09-12T10:55:04,943 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, 2023-09-12T10:55:04,944 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:04,944 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,945 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,946 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,947 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,948 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:04,949 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:04,949 | ^~~~~~~~~~ 2023-09-12T10:55:04,950 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:04,950 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:04,951 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:55:04,952 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, 2023-09-12T10:55:04,952 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, 2023-09-12T10:55:04,953 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, 2023-09-12T10:55:04,953 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:04,954 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,955 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:04,956 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,957 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,958 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:04,958 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:04,959 | ^~~~~~~~~~ 2023-09-12T10:55:04,960 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:55:04,961 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2023-09-12T10:55:04,961 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, 2023-09-12T10:55:04,962 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, 2023-09-12T10:55:04,963 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, 2023-09-12T10:55:04,964 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:04,964 include/openbabel/forcefield.h:170:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,965 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:55:04,966 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,966 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,967 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:04,968 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:04,968 | ^~~~~~~~~~ 2023-09-12T10:55:04,969 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:04,970 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, 2023-09-12T10:55:04,971 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, 2023-09-12T10:55:04,971 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, 2023-09-12T10:55:04,972 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:04,973 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,974 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:04,975 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,977 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,977 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:04,978 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:04,979 | ^~~~~~~~~~ 2023-09-12T10:55:04,980 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:04,980 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, 2023-09-12T10:55:04,981 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, 2023-09-12T10:55:04,982 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, 2023-09-12T10:55:04,983 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:04,984 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,984 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:04,985 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,985 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,986 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:04,987 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:04,987 | ^~~~~~~~~~ 2023-09-12T10:55:04,988 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:04,988 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, 2023-09-12T10:55:04,989 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, 2023-09-12T10:55:04,990 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, 2023-09-12T10:55:04,990 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:04,991 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:04,992 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:04,993 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:04,993 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:04,994 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:04,995 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:04,996 | ^~~~~~~~~~ 2023-09-12T10:55:04,996 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:04,997 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, 2023-09-12T10:55:04,998 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, 2023-09-12T10:55:04,999 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, 2023-09-12T10:55:05,000 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,000 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,001 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,002 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,002 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,003 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,003 | ^~~~~~~~~~ 2023-09-12T10:55:05,004 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,004 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, 2023-09-12T10:55:05,005 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, 2023-09-12T10:55:05,006 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, 2023-09-12T10:55:05,006 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,007 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,008 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,008 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,009 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,010 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,010 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,011 | ^~~~~~~~~~ 2023-09-12T10:55:05,012 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,012 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, 2023-09-12T10:55:05,013 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, 2023-09-12T10:55:05,014 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, 2023-09-12T10:55:05,014 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,015 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,016 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,016 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,017 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,018 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,019 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,019 | ^~~~~~~~~~ 2023-09-12T10:55:05,020 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,021 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, 2023-09-12T10:55:05,022 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, 2023-09-12T10:55:05,022 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, 2023-09-12T10:55:05,023 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,024 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,025 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,026 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,027 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,027 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,028 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,029 | ^~~~~~~~~~ 2023-09-12T10:55:05,029 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,030 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, 2023-09-12T10:55:05,031 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, 2023-09-12T10:55:05,032 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, 2023-09-12T10:55:05,033 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,034 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,034 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,035 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,036 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,036 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,037 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,038 | ^~~~~~~~~~ 2023-09-12T10:55:05,038 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,039 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, 2023-09-12T10:55:05,039 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, 2023-09-12T10:55:05,040 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, 2023-09-12T10:55:05,041 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,042 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,043 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,043 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,044 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,045 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,045 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,046 | ^~~~~~~~~~ 2023-09-12T10:55:05,047 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,048 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, 2023-09-12T10:55:05,048 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, 2023-09-12T10:55:05,049 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, 2023-09-12T10:55:05,050 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,050 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,051 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,052 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,052 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,053 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,053 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,053 | ^~~~~~~~~~ 2023-09-12T10:55:05,054 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,054 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, 2023-09-12T10:55:05,055 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, 2023-09-12T10:55:05,056 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, 2023-09-12T10:55:05,057 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,058 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,058 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,059 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,060 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,060 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,061 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,062 | ^~~~~~~~~~ 2023-09-12T10:55:05,063 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,064 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, 2023-09-12T10:55:05,065 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, 2023-09-12T10:55:05,065 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, 2023-09-12T10:55:05,066 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,067 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,067 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,068 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,069 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,070 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,070 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,071 | ^~~~~~~~~~ 2023-09-12T10:55:05,072 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2023-09-12T10:55:05,072 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, 2023-09-12T10:55:05,073 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, 2023-09-12T10:55:05,074 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, 2023-09-12T10:55:05,075 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,076 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,076 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2023-09-12T10:55:05,077 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,078 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,079 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2023-09-12T10:55:05,080 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2023-09-12T10:55:05,080 | ^~~~~~~~~~ 2023-09-12T10:55:05,081 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:05,082 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:05,083 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:55:05,083 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:55:05,084 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, 2023-09-12T10:55:05,084 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, 2023-09-12T10:55:05,085 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, 2023-09-12T10:55:05,085 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,086 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,086 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:05,087 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,088 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,088 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:55:05,089 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:55:05,089 | ^~~~~~~~~~~ 2023-09-12T10:55:05,090 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:05,091 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:05,091 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:55:05,092 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:55:05,093 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, 2023-09-12T10:55:05,093 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, 2023-09-12T10:55:05,094 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, 2023-09-12T10:55:05,094 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,095 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,096 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:05,096 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,097 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,097 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:55:05,098 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:55:05,098 | ^~~~~~~~~~~ 2023-09-12T10:55:05,099 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:05,099 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:05,100 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:55:05,100 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:55:05,101 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, 2023-09-12T10:55:05,101 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, 2023-09-12T10:55:05,102 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, 2023-09-12T10:55:05,104 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,105 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,106 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:05,106 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,107 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,108 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:55:05,108 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:55:05,109 | ^~~~~~~~~~~ 2023-09-12T10:55:05,110 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2023-09-12T10:55:05,111 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:55:05,111 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:55:05,112 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, 2023-09-12T10:55:05,113 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, 2023-09-12T10:55:05,113 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, 2023-09-12T10:55:05,114 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,114 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,115 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2023-09-12T10:55:05,115 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,116 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,117 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:55:05,118 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:55:05,119 | ^~~~~~~~~~~ 2023-09-12T10:55:05,119 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2023-09-12T10:55:05,120 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2023-09-12T10:55:05,121 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, 2023-09-12T10:55:05,122 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, 2023-09-12T10:55:05,123 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, 2023-09-12T10:55:05,124 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,125 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,125 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2023-09-12T10:55:05,126 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,127 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,128 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:55:05,128 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:55:05,129 | ^~~~~~~~~~~ 2023-09-12T10:55:05,129 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’, 2023-09-12T10:55:05,130 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, 2023-09-12T10:55:05,130 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, 2023-09-12T10:55:05,131 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, 2023-09-12T10:55:05,131 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,132 include/forcefields/forcefieldmmff94.h:61:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::tor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,133 61 | class OBFFTorsionCalculationMMFF94 : public OBFFCalculation4 2023-09-12T10:55:05,133 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,134 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,135 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:55:05,135 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:55:05,136 | ^~~~~~~~~~~ 2023-09-12T10:55:05,137 In copy constructor ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’, 2023-09-12T10:55:05,138 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, 2023-09-12T10:55:05,138 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, 2023-09-12T10:55:05,139 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, 2023-09-12T10:55:05,140 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,141 include/forcefields/forcefieldmmff94.h:61:9: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::cosine’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,141 61 | class OBFFTorsionCalculationMMFF94 : public OBFFCalculation4 2023-09-12T10:55:05,142 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,143 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,143 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2023-09-12T10:55:05,144 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2023-09-12T10:55:05,144 | ^~~~~~~~~~~ 2023-09-12T10:55:05,145 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:05,146 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:05,146 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:55:05,147 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationMMFF94::OBFFOOPCalculationMMFF94(const OpenBabel::OBFFOOPCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:70:9, 2023-09-12T10:55:05,148 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, 2023-09-12T10:55:05,148 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, 2023-09-12T10:55:05,149 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, 2023-09-12T10:55:05,150 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:55:05,151 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,152 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:05,152 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,153 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,154 ./src/forcefields/forcefieldmmff94.cpp:3349:30: note: ‘oopcalc’ declared here 2023-09-12T10:55:05,155 3349 | OBFFOOPCalculationMMFF94 oopcalc; 2023-09-12T10:55:05,155 | ^~~~~~~ 2023-09-12T10:55:05,156 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:05,157 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:05,158 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:55:05,158 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationMMFF94::OBFFOOPCalculationMMFF94(const OpenBabel::OBFFOOPCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:70:9, 2023-09-12T10:55:05,159 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, 2023-09-12T10:55:05,160 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, 2023-09-12T10:55:05,161 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, 2023-09-12T10:55:05,162 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:55:05,162 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,163 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:05,164 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,164 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,165 ./src/forcefields/forcefieldmmff94.cpp:3349:30: note: ‘oopcalc’ declared here 2023-09-12T10:55:05,165 3349 | OBFFOOPCalculationMMFF94 oopcalc; 2023-09-12T10:55:05,166 | ^~~~~~~ 2023-09-12T10:55:05,166 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:05,167 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2023-09-12T10:55:05,167 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2023-09-12T10:55:05,168 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationMMFF94::OBFFOOPCalculationMMFF94(const OpenBabel::OBFFOOPCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:70:9, 2023-09-12T10:55:05,169 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, 2023-09-12T10:55:05,170 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, 2023-09-12T10:55:05,170 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, 2023-09-12T10:55:05,171 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:55:05,172 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:05,173 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:05,173 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:05,174 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2023-09-12T10:55:05,175 ./src/forcefields/forcefieldmmff94.cpp:3349:30: note: ‘oopcalc’ declared here 2023-09-12T10:55:05,176 3349 | OBFFOOPCalculationMMFF94 oopcalc; 2023-09-12T10:55:05,177 | ^~~~~~~ 2023-09-12T10:55:05,177 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,178 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2023-09-12T10:55:05,179 /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 2023-09-12T10:55:05,179 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,180 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,180 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,181 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2023-09-12T10:55:05,182 /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 2023-09-12T10:55:05,182 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,183 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,183 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,184 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2023-09-12T10:55:05,185 /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 2023-09-12T10:55:05,186 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,187 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,188 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,189 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2023-09-12T10:55:05,189 /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 2023-09-12T10:55:05,190 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,191 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,192 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,192 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2023-09-12T10:55:05,193 /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 2023-09-12T10:55:05,194 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,195 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,196 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,197 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3419:41: 2023-09-12T10:55:05,197 /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 2023-09-12T10:55:05,198 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,198 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,199 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,200 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3426:41: 2023-09-12T10:55:05,201 /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 2023-09-12T10:55:05,201 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,202 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,203 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,204 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3434:41: 2023-09-12T10:55:05,205 /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 2023-09-12T10:55:05,205 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,206 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,207 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,208 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3599:33: 2023-09-12T10:55:05,209 /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 2023-09-12T10:55:05,209 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,210 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:05,210 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationMMFF94; _Alloc = std::allocator]’, 2023-09-12T10:55:05,211 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3661:45: 2023-09-12T10:55:05,212 /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 2023-09-12T10:55:05,212 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:05,213 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:07,825 /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]’: 2023-09-12T10:55:07,826 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:07,827 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:55:07,827 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:08,619 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:08,620 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, 2023-09-12T10:55:08,620 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamPbci(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1262:32: 2023-09-12T10:55:08,621 /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 2023-09-12T10:55:08,621 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:08,622 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:08,622 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:08,623 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, 2023-09-12T10:55:08,624 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamPbci(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1263:32: 2023-09-12T10:55:08,624 /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 2023-09-12T10:55:08,625 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:08,626 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:08,899 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:08,900 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, 2023-09-12T10:55:08,900 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamCharge(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1230:32: 2023-09-12T10:55:08,901 /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 2023-09-12T10:55:08,902 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:08,902 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:09,187 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:09,188 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, 2023-09-12T10:55:09,188 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBndk(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:974:32: 2023-09-12T10:55:09,189 /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 2023-09-12T10:55:09,190 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:09,191 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:09,191 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:09,191 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, 2023-09-12T10:55:09,192 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBndk(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:975:32: 2023-09-12T10:55:09,192 /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 2023-09-12T10:55:09,193 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:09,193 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:09,476 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:09,477 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, 2023-09-12T10:55:09,477 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamOOP(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1117:32: 2023-09-12T10:55:09,478 /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 2023-09-12T10:55:09,479 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:09,479 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:09,763 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:09,764 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, 2023-09-12T10:55:09,764 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamDfsb(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1081:32: 2023-09-12T10:55:09,765 /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 2023-09-12T10:55:09,766 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:09,766 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:09,767 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:09,767 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, 2023-09-12T10:55:09,768 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamDfsb(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1082:32: 2023-09-12T10:55:09,769 /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 2023-09-12T10:55:09,769 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:09,771 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:10,060 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:10,060 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, 2023-09-12T10:55:10,061 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBond(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:940:32: 2023-09-12T10:55:10,061 /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 2023-09-12T10:55:10,062 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:10,062 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:10,063 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:10,063 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, 2023-09-12T10:55:10,064 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamBond(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:941:32: 2023-09-12T10:55:10,064 /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 2023-09-12T10:55:10,065 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:10,066 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:10,673 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:10,674 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, 2023-09-12T10:55:10,675 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamStrBnd(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1046:32: 2023-09-12T10:55:10,675 /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 2023-09-12T10:55:10,676 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:10,677 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:10,677 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:10,678 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, 2023-09-12T10:55:10,679 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamStrBnd(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1047:32: 2023-09-12T10:55:10,679 /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 2023-09-12T10:55:10,680 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:10,681 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:10,981 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:10,982 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, 2023-09-12T10:55:10,982 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamAngle(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1010:32: 2023-09-12T10:55:10,983 /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 2023-09-12T10:55:10,983 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:10,984 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:10,984 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:10,985 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, 2023-09-12T10:55:10,985 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamAngle(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1011:32: 2023-09-12T10:55:10,986 /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 2023-09-12T10:55:10,986 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:10,987 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:11,297 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:11,298 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, 2023-09-12T10:55:11,298 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1187:32: 2023-09-12T10:55:11,299 /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 2023-09-12T10:55:11,300 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:11,300 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:11,301 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:11,302 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, 2023-09-12T10:55:11,303 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1188:32: 2023-09-12T10:55:11,303 /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 2023-09-12T10:55:11,304 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:11,304 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:11,305 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:11,306 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, 2023-09-12T10:55:11,307 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1189:32: 2023-09-12T10:55:11,308 /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 2023-09-12T10:55:11,308 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:11,309 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:11,309 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:11,309 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, 2023-09-12T10:55:11,310 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamVDW(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1190:32: 2023-09-12T10:55:11,310 /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 2023-09-12T10:55:11,311 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:11,311 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:11,639 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:11,640 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, 2023-09-12T10:55:11,641 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamTorsion(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1153:32: 2023-09-12T10:55:11,641 /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 2023-09-12T10:55:11,642 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:11,642 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:11,643 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:11,643 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, 2023-09-12T10:55:11,644 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamTorsion(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1154:32: 2023-09-12T10:55:11,645 /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 2023-09-12T10:55:11,645 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:11,646 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:11,647 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:11,648 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, 2023-09-12T10:55:11,648 inlined from ‘bool OpenBabel::OBForceFieldMMFF94::ParseParamTorsion(std::string&)’ at ./src/forcefields/forcefieldmmff94.cpp:1155:32: 2023-09-12T10:55:11,649 /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 2023-09-12T10:55:11,650 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:11,651 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,097 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’: 2023-09-12T10:55:17,098 ./src/forcefields/forcefieldmmff94.cpp:4312:15: warning: ‘eeq’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,098 4312 | snprintf(_logbuf, BUFF_SIZE, "Electrostatic %11.5f %11.5f %11.5f", E_Electrostatic(), eeq, delta); 2023-09-12T10:55:17,099 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,099 ./src/forcefields/forcefieldmmff94.cpp:3989:58: note: ‘eeq’ was declared here 2023-09-12T10:55:17,100 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,100 | ^~~ 2023-09-12T10:55:17,101 ./src/forcefields/forcefieldmmff94.cpp:4308:15: warning: ‘evdw’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,101 4308 | snprintf(_logbuf, BUFF_SIZE, "Van der Waals %11.5f %11.5f %11.5f", E_VDW(), evdw, delta); 2023-09-12T10:55:17,102 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,102 ./src/forcefields/forcefieldmmff94.cpp:3989:52: note: ‘evdw’ was declared here 2023-09-12T10:55:17,103 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,103 | ^~~~ 2023-09-12T10:55:17,104 ./src/forcefields/forcefieldmmff94.cpp:4304:15: warning: ‘etor’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,105 4304 | snprintf(_logbuf, BUFF_SIZE, "Torsional %11.5f %11.5f %11.5f", E_Torsion(), etor, delta); 2023-09-12T10:55:17,106 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,106 ./src/forcefields/forcefieldmmff94.cpp:3989:46: note: ‘etor’ was declared here 2023-09-12T10:55:17,107 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,108 | ^~~~ 2023-09-12T10:55:17,109 ./src/forcefields/forcefieldmmff94.cpp:4296:15: warning: ‘estbn’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,109 4296 | snprintf(_logbuf, BUFF_SIZE, "Stretch-Bending %11.5f %11.5f %11.5f", E_StrBnd(), estbn, delta); 2023-09-12T10:55:17,110 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,111 ./src/forcefields/forcefieldmmff94.cpp:3989:39: note: ‘estbn’ was declared here 2023-09-12T10:55:17,111 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,112 | ^~~~~ 2023-09-12T10:55:17,112 ./src/forcefields/forcefieldmmff94.cpp:4300:15: warning: ‘eoop’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,113 4300 | snprintf(_logbuf, BUFF_SIZE, "Out-Of-Plane Bending %11.5f %11.5f %11.5f", E_OOP(), eoop, delta); 2023-09-12T10:55:17,114 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,114 ./src/forcefields/forcefieldmmff94.cpp:3989:33: note: ‘eoop’ was declared here 2023-09-12T10:55:17,115 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,116 | ^~~~ 2023-09-12T10:55:17,117 ./src/forcefields/forcefieldmmff94.cpp:4292:15: warning: ‘eangle’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,117 4292 | snprintf(_logbuf, BUFF_SIZE, "Angle Bending %11.5f %11.5f %11.5f", E_Angle(), eangle, delta); 2023-09-12T10:55:17,118 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,118 ./src/forcefields/forcefieldmmff94.cpp:3989:25: note: ‘eangle’ was declared here 2023-09-12T10:55:17,119 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,119 | ^~~~~~ 2023-09-12T10:55:17,120 ./src/forcefields/forcefieldmmff94.cpp:4288:15: warning: ‘ebond’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,120 4288 | snprintf(_logbuf, BUFF_SIZE, "Bond Stretching %11.5f %11.5f %11.5f", E_Bond(), ebond, delta); 2023-09-12T10:55:17,121 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,121 ./src/forcefields/forcefieldmmff94.cpp:3989:18: note: ‘ebond’ was declared here 2023-09-12T10:55:17,122 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,122 | ^~~~~ 2023-09-12T10:55:17,123 ./src/forcefields/forcefieldmmff94.cpp:4317:15: warning: ‘etot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:17,123 4317 | snprintf(_logbuf, BUFF_SIZE, "Total ENERGY %11.5f %11.5f %11.5f", Energy(), etot, delta); 2023-09-12T10:55:17,124 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,124 ./src/forcefields/forcefieldmmff94.cpp:3989:12: note: ‘etot’ was declared here 2023-09-12T10:55:17,125 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2023-09-12T10:55:17,126 | ^~~~ 2023-09-12T10:55:17,161 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,162 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, 2023-09-12T10:55:17,163 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4087:31: 2023-09-12T10:55:17,163 /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 2023-09-12T10:55:17,164 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,165 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,165 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,166 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, 2023-09-12T10:55:17,167 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4088:31: 2023-09-12T10:55:17,167 /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 2023-09-12T10:55:17,168 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,169 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,169 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,170 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, 2023-09-12T10:55:17,171 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4089:31: 2023-09-12T10:55:17,171 /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 2023-09-12T10:55:17,172 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,172 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,173 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,173 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, 2023-09-12T10:55:17,174 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4090:31: 2023-09-12T10:55:17,174 /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 2023-09-12T10:55:17,175 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,175 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,176 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,177 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, 2023-09-12T10:55:17,178 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4093:33: 2023-09-12T10:55:17,178 /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 2023-09-12T10:55:17,179 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,180 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,180 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,181 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, 2023-09-12T10:55:17,182 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4095:33: 2023-09-12T10:55:17,183 /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 2023-09-12T10:55:17,183 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,184 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,184 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,185 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, 2023-09-12T10:55:17,186 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4097:33: 2023-09-12T10:55:17,186 /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 2023-09-12T10:55:17,187 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,188 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,188 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,189 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, 2023-09-12T10:55:17,189 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4106:31: 2023-09-12T10:55:17,190 /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 2023-09-12T10:55:17,190 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,191 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,191 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,192 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, 2023-09-12T10:55:17,192 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4107:31: 2023-09-12T10:55:17,193 /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 2023-09-12T10:55:17,194 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,194 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,195 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,196 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, 2023-09-12T10:55:17,197 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4108:31: 2023-09-12T10:55:17,197 /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 2023-09-12T10:55:17,198 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,199 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,199 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,200 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, 2023-09-12T10:55:17,201 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4109:31: 2023-09-12T10:55:17,201 /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 2023-09-12T10:55:17,202 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,203 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,203 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,204 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, 2023-09-12T10:55:17,204 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4112:33: 2023-09-12T10:55:17,205 /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 2023-09-12T10:55:17,206 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,206 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,207 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,207 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, 2023-09-12T10:55:17,208 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4114:33: 2023-09-12T10:55:17,208 /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 2023-09-12T10:55:17,209 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,209 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,210 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,211 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, 2023-09-12T10:55:17,212 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4116:33: 2023-09-12T10:55:17,212 /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 2023-09-12T10:55:17,213 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,214 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:17,214 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:17,215 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, 2023-09-12T10:55:17,216 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’ at ./src/forcefields/forcefieldmmff94.cpp:4137:33: 2023-09-12T10:55:17,217 /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 2023-09-12T10:55:17,217 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:17,218 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:20,727 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/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/' 2023-09-12T10:55:20,728 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/ccjrpli3.s 2023-09-12T10:55:20,737 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:22,474 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/ 2023-09-12T10:55:22,474 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/ 2023-09-12T10:55:22,475 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/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.' 2023-09-12T10:55:22,482 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/forcefields/forcefielduff.cpp -o build/temp.linux-armv7l-cpython-311/./src/forcefields/forcefielduff.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:22,486 Using built-in specs. 2023-09-12T10:55:22,487 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:22,488 Target: arm-linux-gnueabihf 2023-09-12T10:55:22,488 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 2023-09-12T10:55:22,489 Thread model: posix 2023-09-12T10:55:22,489 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:22,490 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:22,491 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/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/' 2023-09-12T10:55:22,491 /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/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/ccXayPjj.s 2023-09-12T10:55:22,502 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:22,502 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 2023-09-12T10:55:22,503 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:22,504 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:22,504 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:22,505 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:22,505 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:22,506 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:22,506 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:22,507 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:22,508 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:22,508 #include "..." search starts here: 2023-09-12T10:55:22,509 #include <...> search starts here: 2023-09-12T10:55:22,510 /usr/include/eigen3 2023-09-12T10:55:22,510 include 2023-09-12T10:55:22,511 /usr/include/python3.11 2023-09-12T10:55:22,512 /usr/include/c++/12 2023-09-12T10:55:22,512 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:22,513 /usr/include/c++/12/backward 2023-09-12T10:55:22,514 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:22,514 /usr/local/include 2023-09-12T10:55:22,515 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:22,515 /usr/include 2023-09-12T10:55:22,516 End of search list. 2023-09-12T10:55:22,517 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:22,517 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:22,518 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:22,519 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:22,521 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:24,092 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:24,092 from include/openbabel/mol.h:43, 2023-09-12T10:55:24,093 from ./src/forcefields/forcefielduff.cpp:21: 2023-09-12T10:55:24,094 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:24,095 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:24,095 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:24,096 | ^ 2023-09-12T10:55:24,097 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:24,098 37 | # define UNUSED(x) x 2023-09-12T10:55:24,098 | ^ 2023-09-12T10:55:24,858 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:24,859 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:24,860 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:24,860 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:24,861 | ^ 2023-09-12T10:55:24,861 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:24,862 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:24,862 | ^~~~~~~~ 2023-09-12T10:55:24,864 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:24,864 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:24,865 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:24,865 | ^ 2023-09-12T10:55:24,866 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:24,867 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:24,867 | ^~~~~~~~ 2023-09-12T10:55:24,882 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:24,883 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:24,884 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:24,885 | ^ 2023-09-12T10:55:24,886 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:24,887 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:24,887 | ^~~~~~~~ 2023-09-12T10:55:24,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:24,890 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:24,890 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:24,891 | ^ 2023-09-12T10:55:24,892 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:24,892 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:24,893 | ^~~~~~~~ 2023-09-12T10:55:25,202 In file included from include/openbabel/forcefield.h:32, 2023-09-12T10:55:25,203 from include/forcefields/forcefielduff.h:24, 2023-09-12T10:55:25,204 from ./src/forcefields/forcefielduff.cpp:24: 2023-09-12T10:55:25,205 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:25,205 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:25,206 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:25,207 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:25,207 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:25,208 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:25,208 from include/openbabel/mol.h:35: 2023-09-12T10:55:25,209 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:25,210 131 | struct binary_function 2023-09-12T10:55:25,210 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:25,330 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T10:55:25,331 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,331 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,332 | ^ 2023-09-12T10:55:25,332 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,333 37 | # define UNUSED(x) x 2023-09-12T10:55:25,334 | ^ 2023-09-12T10:55:25,335 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T10:55:25,335 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,336 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,337 | ^ 2023-09-12T10:55:25,338 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,339 37 | # define UNUSED(x) x 2023-09-12T10:55:25,340 | ^ 2023-09-12T10:55:25,341 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T10:55:25,341 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,342 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,343 | ^ 2023-09-12T10:55:25,344 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,345 37 | # define UNUSED(x) x 2023-09-12T10:55:25,345 | ^ 2023-09-12T10:55:25,346 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T10:55:25,347 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,348 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,348 | ^ 2023-09-12T10:55:25,349 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,350 37 | # define UNUSED(x) x 2023-09-12T10:55:25,351 | ^ 2023-09-12T10:55:25,351 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T10:55:25,352 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,353 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,354 | ^ 2023-09-12T10:55:25,355 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,355 37 | # define UNUSED(x) x 2023-09-12T10:55:25,356 | ^ 2023-09-12T10:55:25,356 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T10:55:25,357 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,357 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,358 | ^ 2023-09-12T10:55:25,359 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,359 37 | # define UNUSED(x) x 2023-09-12T10:55:25,360 | ^ 2023-09-12T10:55:25,360 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T10:55:25,361 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,362 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,362 | ^ 2023-09-12T10:55:25,363 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,363 37 | # define UNUSED(x) x 2023-09-12T10:55:25,364 | ^ 2023-09-12T10:55:25,365 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T10:55:25,365 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T10:55:25,366 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T10:55:25,367 | ^ 2023-09-12T10:55:25,368 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:25,368 37 | # define UNUSED(x) x 2023-09-12T10:55:25,369 | ^ 2023-09-12T10:55:26,287 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = true]’: 2023-09-12T10:55:26,288 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = true]’ 2023-09-12T10:55:26,288 include/forcefields/forcefielduff.h:192:37: required from here 2023-09-12T10:55:26,289 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-12T10:55:26,290 423 | double ab[3]; 2023-09-12T10:55:26,291 | ^~ 2023-09-12T10:55:26,291 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = false]’: 2023-09-12T10:55:26,292 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = false]’ 2023-09-12T10:55:26,293 include/forcefields/forcefielduff.h:192:54: required from here 2023-09-12T10:55:26,293 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-12T10:55:33,311 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:55:33,311 /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]’: 2023-09-12T10:55:33,312 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:33,313 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:55:33,314 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:33,458 /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]’: 2023-09-12T10:55:33,459 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:33,642 /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]’: 2023-09-12T10:55:33,643 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:33,903 /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]’: 2023-09-12T10:55:33,903 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:34,141 /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]’: 2023-09-12T10:55:34,142 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:35,378 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:35,379 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2023-09-12T10:55:35,380 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, 2023-09-12T10:55:35,380 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, 2023-09-12T10:55:35,381 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, 2023-09-12T10:55:35,382 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:55:35,382 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:35,383 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:35,384 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:35,385 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:55:35,385 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:55:35,386 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:55:35,387 | ^~~~~~~~ 2023-09-12T10:55:35,387 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:35,388 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2023-09-12T10:55:35,388 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, 2023-09-12T10:55:35,389 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, 2023-09-12T10:55:35,389 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, 2023-09-12T10:55:35,390 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:55:35,391 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:35,392 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:35,392 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:35,393 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:55:35,394 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:55:35,395 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:55:35,396 | ^~~~~~~~ 2023-09-12T10:55:35,397 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:35,397 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2023-09-12T10:55:35,398 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, 2023-09-12T10:55:35,399 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, 2023-09-12T10:55:35,400 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, 2023-09-12T10:55:35,401 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:55:35,401 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:35,402 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:35,404 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:35,404 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:55:35,405 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:55:35,405 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:55:35,406 | ^~~~~~~~ 2023-09-12T10:55:35,407 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2023-09-12T10:55:35,407 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, 2023-09-12T10:55:35,408 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, 2023-09-12T10:55:35,409 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, 2023-09-12T10:55:35,409 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:55:35,410 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:35,411 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2023-09-12T10:55:35,411 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:35,412 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:55:35,413 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:55:35,414 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:55:35,415 | ^~~~~~~~ 2023-09-12T10:55:35,415 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2023-09-12T10:55:35,416 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, 2023-09-12T10:55:35,417 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, 2023-09-12T10:55:35,418 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, 2023-09-12T10:55:35,419 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:55:35,420 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:35,421 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2023-09-12T10:55:35,422 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:35,423 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2023-09-12T10:55:35,424 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2023-09-12T10:55:35,424 737 | OBFFBondCalculationUFF bondcalc; 2023-09-12T10:55:35,425 | ^~~~~~~~ 2023-09-12T10:55:35,458 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:55:35,458 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,459 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2023-09-12T10:55:35,459 /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 2023-09-12T10:55:35,460 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,461 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:35,464 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,464 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:979:37: 2023-09-12T10:55:35,465 /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 2023-09-12T10:55:35,465 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,466 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:35,467 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,467 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2023-09-12T10:55:35,468 /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 2023-09-12T10:55:35,469 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,470 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:35,474 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,475 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1273:37: 2023-09-12T10:55:35,476 /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 2023-09-12T10:55:35,476 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,477 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:35,479 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,480 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1395:33: 2023-09-12T10:55:35,481 /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 2023-09-12T10:55:35,481 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,482 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:35,483 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,484 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1402:33: 2023-09-12T10:55:35,484 /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 2023-09-12T10:55:35,485 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,485 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:35,486 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,486 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1410:33: 2023-09-12T10:55:35,487 /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 2023-09-12T10:55:35,487 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,488 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:35,488 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:35,489 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1454:35: 2023-09-12T10:55:35,490 /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 2023-09-12T10:55:35,491 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:35,491 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:38,497 /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]’: 2023-09-12T10:55:38,498 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:38,499 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:55:38,500 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:38,669 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:38,670 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2023-09-12T10:55:38,671 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, 2023-09-12T10:55:38,671 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, 2023-09-12T10:55:38,672 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, 2023-09-12T10:55:38,673 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:55:38,674 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:38,674 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:38,675 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:38,676 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:55:38,676 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:55:38,677 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:55:38,677 | ^~~~~~~ 2023-09-12T10:55:38,678 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:38,678 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2023-09-12T10:55:38,679 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, 2023-09-12T10:55:38,680 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, 2023-09-12T10:55:38,681 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, 2023-09-12T10:55:38,681 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:55:38,682 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:38,683 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:38,683 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:38,684 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:55:38,685 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:55:38,685 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:55:38,686 | ^~~~~~~ 2023-09-12T10:55:38,687 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2023-09-12T10:55:38,687 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2023-09-12T10:55:38,688 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, 2023-09-12T10:55:38,689 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, 2023-09-12T10:55:38,690 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, 2023-09-12T10:55:38,690 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:55:38,691 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:38,692 139 | class OBFPRT OBFFCalculation2 2023-09-12T10:55:38,692 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:55:38,693 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:55:38,693 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:55:38,694 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:55:38,695 | ^~~~~~~ 2023-09-12T10:55:38,695 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’, 2023-09-12T10:55:38,696 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, 2023-09-12T10:55:38,696 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, 2023-09-12T10:55:38,697 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, 2023-09-12T10:55:38,698 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:55:38,698 include/forcefields/forcefielduff.h:82:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:55:38,699 82 | class OBFFElectrostaticCalculationUFF : public OBFFCalculation2 2023-09-12T10:55:38,700 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:38,701 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2023-09-12T10:55:38,701 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2023-09-12T10:55:38,702 1475 | OBFFElectrostaticCalculationUFF elecalc; 2023-09-12T10:55:38,703 | ^~~~~~~ 2023-09-12T10:55:38,704 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’, 2023-09-12T10:55:38,704 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2023-09-12T10:55:38,706 /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 2023-09-12T10:55:38,706 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:55:38,707 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:55:38,956 /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]’: 2023-09-12T10:55:38,957 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:55:38,957 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:55:38,958 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,227 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,228 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, 2023-09-12T10:55:42,229 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1576:34: 2023-09-12T10:55:42,229 /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 2023-09-12T10:55:42,230 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,231 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,232 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,232 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, 2023-09-12T10:55:42,233 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1577:34: 2023-09-12T10:55:42,234 /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 2023-09-12T10:55:42,235 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,235 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,236 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,237 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, 2023-09-12T10:55:42,237 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1578:34: 2023-09-12T10:55:42,238 /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 2023-09-12T10:55:42,239 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,240 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,241 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,242 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, 2023-09-12T10:55:42,242 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1579:34: 2023-09-12T10:55:42,243 /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 2023-09-12T10:55:42,243 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,244 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,245 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,245 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, 2023-09-12T10:55:42,246 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1580:34: 2023-09-12T10:55:42,246 /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 2023-09-12T10:55:42,247 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,248 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,248 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,249 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, 2023-09-12T10:55:42,250 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1581:34: 2023-09-12T10:55:42,251 /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 2023-09-12T10:55:42,251 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,252 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,253 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,254 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, 2023-09-12T10:55:42,255 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1582:34: 2023-09-12T10:55:42,255 /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 2023-09-12T10:55:42,256 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,256 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,257 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,258 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, 2023-09-12T10:55:42,258 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1583:34: 2023-09-12T10:55:42,260 /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 2023-09-12T10:55:42,260 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,260 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,261 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,261 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, 2023-09-12T10:55:42,262 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1584:34: 2023-09-12T10:55:42,262 /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 2023-09-12T10:55:42,263 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,263 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,264 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,264 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, 2023-09-12T10:55:42,265 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1585:34: 2023-09-12T10:55:42,266 /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 2023-09-12T10:55:42,267 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,267 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:42,268 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:55:42,269 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, 2023-09-12T10:55:42,270 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::ParseParamFile()’ at ./src/forcefields/forcefielduff.cpp:1586:34: 2023-09-12T10:55:42,271 /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 2023-09-12T10:55:42,271 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:55:42,272 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:44,784 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:55:44,784 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/ccXayPjj.s 2023-09-12T10:55:44,789 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:45,943 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/ 2023-09-12T10:55:45,943 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/ 2023-09-12T10:55:45,944 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/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.' 2023-09-12T10:55:45,949 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 2023-09-12T10:55:45,953 Using built-in specs. 2023-09-12T10:55:45,954 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:45,954 Target: arm-linux-gnueabihf 2023-09-12T10:55:45,955 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 2023-09-12T10:55:45,955 Thread model: posix 2023-09-12T10:55:45,956 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:45,957 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:45,957 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:55:45,958 /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/ccTDm19o.s 2023-09-12T10:55:45,966 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:45,967 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 2023-09-12T10:55:45,968 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:45,968 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:45,969 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:45,969 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:45,970 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:45,970 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:45,971 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:45,971 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:45,972 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:45,972 #include "..." search starts here: 2023-09-12T10:55:45,972 #include <...> search starts here: 2023-09-12T10:55:45,973 /usr/include/eigen3 2023-09-12T10:55:45,973 include 2023-09-12T10:55:45,974 /usr/include/python3.11 2023-09-12T10:55:45,974 /usr/include/c++/12 2023-09-12T10:55:45,975 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:45,975 /usr/include/c++/12/backward 2023-09-12T10:55:45,976 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:45,977 /usr/local/include 2023-09-12T10:55:45,977 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:45,978 /usr/include 2023-09-12T10:55:45,979 End of search list. 2023-09-12T10:55:45,979 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:45,980 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:45,981 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:45,982 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:45,984 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:47,207 In file included from include/openbabel/format.h:22, 2023-09-12T10:55:47,208 from ./src/format.cpp:20: 2023-09-12T10:55:47,208 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:47,209 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:47,210 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:47,210 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:55:47,211 from include/openbabel/plugin.h:23: 2023-09-12T10:55:47,212 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:47,212 131 | struct binary_function 2023-09-12T10:55:47,213 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:48,531 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2023-09-12T10:55:48,532 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/ccTDm19o.s 2023-09-12T10:55:48,537 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:48,635 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/ 2023-09-12T10:55:48,636 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/ 2023-09-12T10:55:48,636 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/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.' 2023-09-12T10:55:48,637 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 2023-09-12T10:55:48,642 Using built-in specs. 2023-09-12T10:55:48,643 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:48,644 Target: arm-linux-gnueabihf 2023-09-12T10:55:48,644 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 2023-09-12T10:55:48,645 Thread model: posix 2023-09-12T10:55:48,645 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:48,646 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:48,647 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/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/' 2023-09-12T10:55:48,647 /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/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/cc056VhH.s 2023-09-12T10:55:48,655 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:48,656 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 2023-09-12T10:55:48,657 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:48,658 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:48,658 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:48,658 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:48,659 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:48,659 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:48,660 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:48,660 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:48,661 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:48,661 #include "..." search starts here: 2023-09-12T10:55:48,662 #include <...> search starts here: 2023-09-12T10:55:48,663 /usr/include/eigen3 2023-09-12T10:55:48,663 include 2023-09-12T10:55:48,664 /usr/include/python3.11 2023-09-12T10:55:48,665 /usr/include/c++/12 2023-09-12T10:55:48,665 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:48,666 /usr/include/c++/12/backward 2023-09-12T10:55:48,667 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:48,667 /usr/local/include 2023-09-12T10:55:48,668 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:48,669 /usr/include 2023-09-12T10:55:48,669 End of search list. 2023-09-12T10:55:48,670 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:48,670 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 2023-09-12T10:55:48,672 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:48,673 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:48,673 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:50,135 In file included from include/openbabel/format.h:22, 2023-09-12T10:55:50,136 from include/openbabel/obconversion.h:37, 2023-09-12T10:55:50,136 from ./src/formats/APIInterface.cpp:19: 2023-09-12T10:55:50,137 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:50,138 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:50,139 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:50,139 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:55:50,140 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:55:50,141 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:55:50,141 from /usr/include/c++/12/ios:42, 2023-09-12T10:55:50,142 from /usr/include/c++/12/ostream:38, 2023-09-12T10:55:50,143 from /usr/include/c++/12/iostream:39, 2023-09-12T10:55:50,144 from include/openbabel/obconversion.h:24: 2023-09-12T10:55:50,145 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:50,145 131 | struct binary_function 2023-09-12T10:55:50,146 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:51,172 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:55:51,173 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/cc056VhH.s 2023-09-12T10:55:51,177 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:51,257 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/ 2023-09-12T10:55:51,257 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/ 2023-09-12T10:55:51,258 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/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.' 2023-09-12T10:55:51,258 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 2023-09-12T10:55:51,263 Using built-in specs. 2023-09-12T10:55:51,264 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:51,265 Target: arm-linux-gnueabihf 2023-09-12T10:55:51,265 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 2023-09-12T10:55:51,266 Thread model: posix 2023-09-12T10:55:51,266 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:51,267 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:51,267 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:55:51,268 /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/ccUxoZjQ.s 2023-09-12T10:55:51,277 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 2023-09-12T10:55:51,278 GNU C17 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:51,279 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:51,280 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:51,280 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:51,281 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:51,281 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:51,282 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:51,282 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:51,283 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:51,283 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:51,284 #include "..." search starts here: 2023-09-12T10:55:51,285 #include <...> search starts here: 2023-09-12T10:55:51,285 /usr/include/eigen3 2023-09-12T10:55:51,286 include 2023-09-12T10:55:51,287 /usr/include/python3.11 2023-09-12T10:55:51,287 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:51,288 /usr/local/include 2023-09-12T10:55:51,288 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:51,289 /usr/include 2023-09-12T10:55:51,290 End of search list. 2023-09-12T10:55:51,290 GNU C17 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:51,291 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 2023-09-12T10:55:51,292 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:51,293 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:51,293 Compiler executable checksum: aa6629b5f44fe3420ba005fbae7bc0e6 2023-09-12T10:55:51,506 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:55:51,507 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/ccUxoZjQ.s 2023-09-12T10:55:51,511 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:51,521 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/ 2023-09-12T10:55:51,522 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/ 2023-09-12T10:55:51,522 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/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.' 2023-09-12T10:55:51,523 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/CSRformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/CSRformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:55:51,526 Using built-in specs. 2023-09-12T10:55:51,527 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:51,528 Target: arm-linux-gnueabihf 2023-09-12T10:55:51,529 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 2023-09-12T10:55:51,529 Thread model: posix 2023-09-12T10:55:51,530 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:51,531 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:51,531 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:55:51,532 /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/ccLG4049.s 2023-09-12T10:55:51,540 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:51,541 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:51,542 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:51,542 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:51,542 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:51,543 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:51,543 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:51,544 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:51,544 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:51,545 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:51,545 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:51,545 #include "..." search starts here: 2023-09-12T10:55:51,546 #include <...> search starts here: 2023-09-12T10:55:51,547 /usr/include/eigen3 2023-09-12T10:55:51,547 include 2023-09-12T10:55:51,548 /usr/include/python3.11 2023-09-12T10:55:51,548 /usr/include/c++/12 2023-09-12T10:55:51,549 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:51,550 /usr/include/c++/12/backward 2023-09-12T10:55:51,550 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:51,551 /usr/local/include 2023-09-12T10:55:51,552 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:51,552 /usr/include 2023-09-12T10:55:51,553 End of search list. 2023-09-12T10:55:51,554 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:51,554 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:55:51,556 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:51,556 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:51,558 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:53,152 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:53,152 from include/openbabel/mol.h:43, 2023-09-12T10:55:53,153 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:55:53,154 from ./src/formats/CSRformat.cpp:17: 2023-09-12T10:55:53,154 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:53,155 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:53,156 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:53,156 | ^ 2023-09-12T10:55:53,157 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:53,158 37 | # define UNUSED(x) x 2023-09-12T10:55:53,158 | ^ 2023-09-12T10:55:53,956 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:53,957 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:53,957 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:53,958 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:53,959 | ^ 2023-09-12T10:55:53,959 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:53,960 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:53,961 | ^~~~~~~~ 2023-09-12T10:55:53,961 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:53,962 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:53,962 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:53,963 | ^ 2023-09-12T10:55:53,964 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:53,964 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:53,965 | ^~~~~~~~ 2023-09-12T10:55:53,980 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:53,981 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:53,982 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:53,983 | ^ 2023-09-12T10:55:53,983 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:53,984 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:53,985 | ^~~~~~~~ 2023-09-12T10:55:53,987 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:53,988 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:53,989 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:53,989 | ^ 2023-09-12T10:55:53,990 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:53,991 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:53,991 | ^~~~~~~~ 2023-09-12T10:55:54,160 In file included from include/openbabel/format.h:22, 2023-09-12T10:55:54,160 from include/openbabel/obconversion.h:37, 2023-09-12T10:55:54,161 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:55:54,162 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:54,163 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:54,164 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:54,165 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:54,165 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:54,166 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:54,166 from include/openbabel/mol.h:35: 2023-09-12T10:55:54,167 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:54,167 131 | struct binary_function 2023-09-12T10:55:54,168 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:56,371 ./src/formats/CSRformat.cpp: In member function ‘char* OpenBabel::CSRFormat::PadString(char*, int)’: 2023-09-12T10:55:56,372 ./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] 2023-09-12T10:55:56,373 188 | strncpy(output, input, strlen(input)); 2023-09-12T10:55:56,373 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:56,583 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:55:56,584 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/ccLG4049.s 2023-09-12T10:55:56,589 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:55:56,723 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/ 2023-09-12T10:55:56,723 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/ 2023-09-12T10:55:56,724 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/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.' 2023-09-12T10:55:56,725 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 2023-09-12T10:55:56,729 Using built-in specs. 2023-09-12T10:55:56,730 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:55:56,730 Target: arm-linux-gnueabihf 2023-09-12T10:55:56,731 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 2023-09-12T10:55:56,732 Thread model: posix 2023-09-12T10:55:56,733 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:55:56,733 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:55:56,734 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:55:56,734 /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/ccnllXPq.s 2023-09-12T10:55:56,742 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:56,743 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 2023-09-12T10:55:56,744 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:56,745 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:56,746 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:55:56,746 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:55:56,747 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:55:56,748 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:55:56,748 ignoring duplicate directory "/usr/include/" 2023-09-12T10:55:56,749 as it is a non-system directory that duplicates a system directory 2023-09-12T10:55:56,749 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:55:56,750 #include "..." search starts here: 2023-09-12T10:55:56,750 #include <...> search starts here: 2023-09-12T10:55:56,751 /usr/include/eigen3 2023-09-12T10:55:56,752 include 2023-09-12T10:55:56,752 /usr/include/python3.11 2023-09-12T10:55:56,753 /usr/include/c++/12 2023-09-12T10:55:56,754 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:55:56,754 /usr/include/c++/12/backward 2023-09-12T10:55:56,755 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:55:56,756 /usr/local/include 2023-09-12T10:55:56,756 /usr/include/arm-linux-gnueabihf 2023-09-12T10:55:56,757 /usr/include 2023-09-12T10:55:56,757 End of search list. 2023-09-12T10:55:56,758 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:55:56,759 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 2023-09-12T10:55:56,760 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:55:56,760 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:55:56,761 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:55:58,329 In file included from include/openbabel/atom.h:33, 2023-09-12T10:55:58,330 from include/openbabel/mol.h:43, 2023-09-12T10:55:58,330 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:55:58,331 from ./src/formats/MCDLformat.cpp:21: 2023-09-12T10:55:58,331 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:55:58,332 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:55:58,332 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:55:58,333 | ^ 2023-09-12T10:55:58,333 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:55:58,334 37 | # define UNUSED(x) x 2023-09-12T10:55:58,334 | ^ 2023-09-12T10:55:59,098 In file included from include/openbabel/mol.h:52: 2023-09-12T10:55:59,098 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:59,099 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:59,099 862 | {return new OBVibrationData(*this);} 2023-09-12T10:55:59,100 | ^ 2023-09-12T10:55:59,101 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:55:59,101 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:55:59,102 | ^~~~~~~~ 2023-09-12T10:55:59,103 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:59,103 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:59,104 907 | {return new OBDOSData(*this);} 2023-09-12T10:55:59,105 | ^ 2023-09-12T10:55:59,106 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:55:59,106 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:55:59,107 | ^~~~~~~~ 2023-09-12T10:55:59,122 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:59,123 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:59,123 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:55:59,124 | ^ 2023-09-12T10:55:59,125 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:55:59,126 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:55:59,127 | ^~~~~~~~ 2023-09-12T10:55:59,128 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:55:59,129 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:55:59,130 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:55:59,130 | ^ 2023-09-12T10:55:59,131 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:55:59,132 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:55:59,132 | ^~~~~~~~ 2023-09-12T10:55:59,301 In file included from include/openbabel/format.h:22, 2023-09-12T10:55:59,302 from include/openbabel/obconversion.h:37, 2023-09-12T10:55:59,302 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:55:59,303 include/openbabel/plugin.h: At global scope: 2023-09-12T10:55:59,303 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:55:59,304 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:55:59,305 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:59,305 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:55:59,306 from /usr/include/c++/12/vector:66, 2023-09-12T10:55:59,307 from include/openbabel/mol.h:35: 2023-09-12T10:55:59,307 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:55:59,308 131 | struct binary_function 2023-09-12T10:55:59,309 | ^~~~~~~~~~~~~~~ 2023-09-12T10:55:59,516 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::constring(int (*)[4], char*)’: 2023-09-12T10:55:59,517 ./src/formats/MCDLformat.cpp:174:66: warning: unused parameter ‘tstr’ [-Wunused-parameter] 2023-09-12T10:55:59,517 174 | string MCDLFormat::constring(int conntab [MAXBONDS][4], char * tstr) 2023-09-12T10:55:59,518 | ~~~~~~~^~~~ 2023-09-12T10:55:59,519 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2023-09-12T10:55:59,520 ./src/formats/MCDLformat.cpp:278:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:55:59,520 278 | if (jflag) 2023-09-12T10:55:59,521 | ^~ 2023-09-12T10:55:59,522 ./src/formats/MCDLformat.cpp:282:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T10:55:59,522 282 | nt = 1; 2023-09-12T10:55:59,523 | ^~ 2023-09-12T10:55:59,569 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::getMCDL(OpenBabel::OBMol*, bool)’: 2023-09-12T10:55:59,570 ./src/formats/MCDLformat.cpp:529:10: warning: variable ‘test’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:55:59,571 529 | bool test;//, testParity; 2023-09-12T10:55:59,571 | ^~~~ 2023-09-12T10:55:59,574 ./src/formats/MCDLformat.cpp:479:48: warning: unused parameter ‘includeCoordinates’ [-Wunused-parameter] 2023-09-12T10:55:59,574 479 | string MCDLFormat::getMCDL(OBMol* pmol, bool includeCoordinates) { 2023-09-12T10:55:59,576 | ~~~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:59,576 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::restoreFullMCDL(std::string, OpenBabel::OBMol*)’: 2023-09-12T10:55:59,577 ./src/formats/MCDLformat.cpp:948:43: warning: unused parameter ‘value’ [-Wunused-parameter] 2023-09-12T10:55:59,577 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2023-09-12T10:55:59,578 | ~~~~~~~^~~~~ 2023-09-12T10:55:59,578 ./src/formats/MCDLformat.cpp:948:57: warning: unused parameter ‘pmol’ [-Wunused-parameter] 2023-09-12T10:55:59,579 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2023-09-12T10:55:59,580 | ~~~~~~~^~~~ 2023-09-12T10:55:59,588 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::setMCDL(std::string, OpenBabel::OBMol*, std::string&)’: 2023-09-12T10:55:59,589 ./src/formats/MCDLformat.cpp:1031:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:55:59,589 1031 | if (n1 < 0) n1=indexOf(s,"-"); 2023-09-12T10:55:59,590 | ~~~^~~ 2023-09-12T10:55:59,591 ./src/formats/MCDLformat.cpp:1032:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:55:59,591 1032 | if (n1 < 0) n1=indexOf(s,"*"); 2023-09-12T10:55:59,592 | ~~~^~~ 2023-09-12T10:55:59,592 ./src/formats/MCDLformat.cpp:1033:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:55:59,593 1033 | if (n1 < 0) { 2023-09-12T10:55:59,594 | ~~~^~~ 2023-09-12T10:55:59,594 ./src/formats/MCDLformat.cpp:1062:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,595 1062 | if (n1>=0) { 2023-09-12T10:55:59,596 | ~~^~~ 2023-09-12T10:55:59,597 ./src/formats/MCDLformat.cpp:1070:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,597 1070 | if (n1>=0) { 2023-09-12T10:55:59,598 | ~~^~~ 2023-09-12T10:55:59,599 ./src/formats/MCDLformat.cpp:1079:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,599 1079 | if (n1>=0) { 2023-09-12T10:55:59,600 | ~~^~~ 2023-09-12T10:55:59,601 ./src/formats/MCDLformat.cpp:1092:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,602 1092 | if (n1>=0) { 2023-09-12T10:55:59,602 | ~~^~~ 2023-09-12T10:55:59,605 ./src/formats/MCDLformat.cpp:1118:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:55:59,606 1118 | if (n1<0) { 2023-09-12T10:55:59,607 | ~~^~ 2023-09-12T10:55:59,607 ./src/formats/MCDLformat.cpp:1121:25: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,608 1121 | if ((n2=0)) n1=n2; 2023-09-12T10:55:59,609 | ~~^~~ 2023-09-12T10:55:59,620 ./src/formats/MCDLformat.cpp:1266:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T10:55:59,621 1266 | if (nPrev == acount) { 2023-09-12T10:55:59,621 | ~~~~~~^~~~~~~~~ 2023-09-12T10:55:59,623 ./src/formats/MCDLformat.cpp:1298:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2023-09-12T10:55:59,624 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2023-09-12T10:55:59,625 | ~~^~ 2023-09-12T10:55:59,626 ./src/formats/MCDLformat.cpp:1298:45: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,626 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2023-09-12T10:55:59,627 | ~~^~~ 2023-09-12T10:55:59,627 ./src/formats/MCDLformat.cpp:1300:12: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,628 1300 | if ((n1>=0) && (value.length() > n1)) { 2023-09-12T10:55:59,628 | ~~^~~ 2023-09-12T10:55:59,629 ./src/formats/MCDLformat.cpp:1312:13: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,630 1312 | if (n1>=0) { 2023-09-12T10:55:59,630 | ~~^~~ 2023-09-12T10:55:59,639 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::indexOf(std::string, std::string, int)’: 2023-09-12T10:55:59,639 ./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] 2023-09-12T10:55:59,640 1384 | if (result == string::npos) result=-1; 2023-09-12T10:55:59,641 | ~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T10:55:59,641 ./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] 2023-09-12T10:55:59,642 1385 | if (result >= instring.length()) result=-1; 2023-09-12T10:55:59,642 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:55:59,643 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::lastIndexOf(std::string, std::string)’: 2023-09-12T10:55:59,644 ./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] 2023-09-12T10:55:59,644 1398 | if (n == string::npos) 2023-09-12T10:55:59,645 | ~~^~~~~~~~~~~~~~~ 2023-09-12T10:55:59,646 ./src/formats/MCDLformat.cpp: In member function ‘bool OpenBabel::MCDLFormat::parseFormula(std::string, std::vector&)’: 2023-09-12T10:55:59,647 ./src/formats/MCDLformat.cpp:1426:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,647 1426 | if (n>=0) { 2023-09-12T10:55:59,648 | ~^~~ 2023-09-12T10:55:59,649 ./src/formats/MCDLformat.cpp:1449:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2023-09-12T10:55:59,650 1449 | if (n>=0) { 2023-09-12T10:55:59,651 | ~^~~ 2023-09-12T10:56:04,047 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2023-09-12T10:56:04,048 ./src/formats/MCDLformat.cpp:237:28: warning: ‘jump’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:04,048 237 | int numdups, dupfrag, jump; 2023-09-12T10:56:04,049 | ^~~~ 2023-09-12T10:56:04,050 ./src/formats/MCDLformat.cpp:395:22: warning: ‘dupfrag’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:04,050 395 | else if (ix[i] == dupfrag && j != dupnum) 2023-09-12T10:56:04,051 | ^~ 2023-09-12T10:56:04,052 ./src/formats/MCDLformat.cpp:237:19: note: ‘dupfrag’ was declared here 2023-09-12T10:56:04,053 237 | int numdups, dupfrag, jump; 2023-09-12T10:56:04,053 | ^~~~~~~ 2023-09-12T10:56:04,054 ./src/formats/MCDLformat.cpp:385:24: warning: ‘numdups’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:04,055 385 | for (j=0; j search starts here: 2023-09-12T10:56:21,208 /usr/include/eigen3 2023-09-12T10:56:21,208 include 2023-09-12T10:56:21,209 /usr/include/python3.11 2023-09-12T10:56:21,210 /usr/include/c++/12 2023-09-12T10:56:21,210 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:21,211 /usr/include/c++/12/backward 2023-09-12T10:56:21,211 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:21,212 /usr/local/include 2023-09-12T10:56:21,213 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:21,213 /usr/include 2023-09-12T10:56:21,214 End of search list. 2023-09-12T10:56:21,214 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:21,215 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:21,216 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:21,216 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:21,217 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:22,777 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:22,778 from include/openbabel/mol.h:43, 2023-09-12T10:56:22,779 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:56:22,779 from ./src/formats/MNAformat.cpp:31: 2023-09-12T10:56:22,780 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:22,781 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:22,782 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:22,782 | ^ 2023-09-12T10:56:22,783 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:22,783 37 | # define UNUSED(x) x 2023-09-12T10:56:22,784 | ^ 2023-09-12T10:56:23,543 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:23,544 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:23,544 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:23,545 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:23,545 | ^ 2023-09-12T10:56:23,546 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:23,547 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:23,547 | ^~~~~~~~ 2023-09-12T10:56:23,548 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:23,549 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:23,550 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:23,550 | ^ 2023-09-12T10:56:23,551 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:23,552 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:23,552 | ^~~~~~~~ 2023-09-12T10:56:23,567 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:23,568 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:23,569 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:23,570 | ^ 2023-09-12T10:56:23,570 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:23,571 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:23,572 | ^~~~~~~~ 2023-09-12T10:56:23,574 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:23,574 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:23,575 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:23,576 | ^ 2023-09-12T10:56:23,576 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:23,577 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:23,578 | ^~~~~~~~ 2023-09-12T10:56:23,746 In file included from include/openbabel/format.h:22, 2023-09-12T10:56:23,747 from include/openbabel/obconversion.h:37, 2023-09-12T10:56:23,747 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:56:23,748 include/openbabel/plugin.h: At global scope: 2023-09-12T10:56:23,748 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:23,749 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:23,749 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:23,750 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:56:23,751 from /usr/include/c++/12/vector:66, 2023-09-12T10:56:23,751 from include/openbabel/mol.h:35: 2023-09-12T10:56:23,752 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:23,752 131 | struct binary_function 2023-09-12T10:56:23,753 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:27,969 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/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/' 2023-09-12T10:56:27,970 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/MNAformat.o /tmp/ccwGwsOi.s 2023-09-12T10:56:27,975 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:28,272 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/ 2023-09-12T10:56:28,273 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/ 2023-09-12T10:56:28,274 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:56:28,275 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 2023-09-12T10:56:28,279 Using built-in specs. 2023-09-12T10:56:28,280 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:28,280 Target: arm-linux-gnueabihf 2023-09-12T10:56:28,281 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 2023-09-12T10:56:28,281 Thread model: posix 2023-09-12T10:56:28,282 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:28,282 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:28,283 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:56:28,283 /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/cc2uGISe.s 2023-09-12T10:56:28,292 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:28,293 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:28,294 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:28,294 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:28,295 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:28,296 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:28,296 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:28,297 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:28,297 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:28,298 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:28,298 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:28,299 #include "..." search starts here: 2023-09-12T10:56:28,299 #include <...> search starts here: 2023-09-12T10:56:28,300 /usr/include/eigen3 2023-09-12T10:56:28,301 include 2023-09-12T10:56:28,301 /usr/include/python3.11 2023-09-12T10:56:28,302 /usr/include/c++/12 2023-09-12T10:56:28,303 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:28,303 /usr/include/c++/12/backward 2023-09-12T10:56:28,304 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:28,305 /usr/local/include 2023-09-12T10:56:28,305 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:28,305 /usr/include 2023-09-12T10:56:28,306 End of search list. 2023-09-12T10:56:28,306 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:28,307 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 2023-09-12T10:56:28,308 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:28,308 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:28,315 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:29,889 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:29,890 from include/openbabel/mol.h:43, 2023-09-12T10:56:29,891 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:56:29,891 from ./src/formats/PQSformat.cpp:16: 2023-09-12T10:56:29,892 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:29,892 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:29,893 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:29,893 | ^ 2023-09-12T10:56:29,894 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:29,894 37 | # define UNUSED(x) x 2023-09-12T10:56:29,895 | ^ 2023-09-12T10:56:30,656 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:30,657 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:30,657 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:30,658 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:30,659 | ^ 2023-09-12T10:56:30,660 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:30,660 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:30,661 | ^~~~~~~~ 2023-09-12T10:56:30,662 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:30,663 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:30,664 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:30,664 | ^ 2023-09-12T10:56:30,665 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:30,666 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:30,666 | ^~~~~~~~ 2023-09-12T10:56:30,682 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:30,682 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:30,683 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:30,684 | ^ 2023-09-12T10:56:30,685 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:30,685 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:30,686 | ^~~~~~~~ 2023-09-12T10:56:30,689 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:30,689 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:30,690 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:30,690 | ^ 2023-09-12T10:56:30,691 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:30,692 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:30,692 | ^~~~~~~~ 2023-09-12T10:56:30,861 In file included from include/openbabel/format.h:22, 2023-09-12T10:56:30,862 from include/openbabel/obconversion.h:37, 2023-09-12T10:56:30,863 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:56:30,864 include/openbabel/plugin.h: At global scope: 2023-09-12T10:56:30,864 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:30,865 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:30,866 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:30,867 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:56:30,868 from /usr/include/c++/12/vector:66, 2023-09-12T10:56:30,868 from include/openbabel/mol.h:35: 2023-09-12T10:56:30,869 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:30,870 131 | struct binary_function 2023-09-12T10:56:30,871 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:33,767 ./src/formats/PQSformat.cpp: In member function ‘virtual bool OpenBabel::PQSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:56:33,768 ./src/formats/PQSformat.cpp:259:49: warning: ‘pFormat’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:33,769 259 | return pFormat->ReadMolecule(&mol,&coordconv); 2023-09-12T10:56:33,769 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:56:33,770 ./src/formats/PQSformat.cpp:250:31: note: ‘pFormat’ was declared here 2023-09-12T10:56:33,771 250 | OBFormat* pFormat; 2023-09-12T10:56:33,771 | ^~~~~~~ 2023-09-12T10:56:34,439 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/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/' 2023-09-12T10:56:34,439 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/formats/PQSformat.o /tmp/cc2uGISe.s 2023-09-12T10:56:34,444 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:34,675 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/ 2023-09-12T10:56:34,675 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/ 2023-09-12T10:56:34,676 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/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.' 2023-09-12T10:56:34,677 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 2023-09-12T10:56:34,681 Using built-in specs. 2023-09-12T10:56:34,682 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:34,683 Target: arm-linux-gnueabihf 2023-09-12T10:56:34,683 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 2023-09-12T10:56:34,684 Thread model: posix 2023-09-12T10:56:34,684 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:34,685 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:34,685 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/' 2023-09-12T10:56:34,686 /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/cceq8GcB.s 2023-09-12T10:56:34,694 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:34,695 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 2023-09-12T10:56:34,696 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:34,697 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:34,697 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:34,697 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:34,698 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:34,698 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:34,699 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:34,699 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:34,700 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:34,700 #include "..." search starts here: 2023-09-12T10:56:34,701 #include <...> search starts here: 2023-09-12T10:56:34,701 /usr/include/eigen3 2023-09-12T10:56:34,702 include 2023-09-12T10:56:34,702 /usr/include/python3.11 2023-09-12T10:56:34,703 /usr/include/c++/12 2023-09-12T10:56:34,704 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:34,704 /usr/include/c++/12/backward 2023-09-12T10:56:34,705 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:34,706 /usr/local/include 2023-09-12T10:56:34,706 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:34,707 /usr/include 2023-09-12T10:56:34,708 End of search list. 2023-09-12T10:56:34,708 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:34,709 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:34,710 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:34,711 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:34,715 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:36,275 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:36,276 from include/openbabel/mol.h:43, 2023-09-12T10:56:36,277 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:56:36,277 from ./src/formats/abinitformat.cpp:16: 2023-09-12T10:56:36,278 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:36,279 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:36,279 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:36,280 | ^ 2023-09-12T10:56:36,281 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:36,281 37 | # define UNUSED(x) x 2023-09-12T10:56:36,282 | ^ 2023-09-12T10:56:37,043 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:37,044 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:37,044 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:37,046 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:37,046 | ^ 2023-09-12T10:56:37,047 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:37,047 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:37,048 | ^~~~~~~~ 2023-09-12T10:56:37,048 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:37,049 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:37,050 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:37,050 | ^ 2023-09-12T10:56:37,051 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:37,051 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:37,052 | ^~~~~~~~ 2023-09-12T10:56:37,068 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:37,068 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:37,069 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:37,070 | ^ 2023-09-12T10:56:37,071 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:37,071 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:37,073 | ^~~~~~~~ 2023-09-12T10:56:37,075 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:37,076 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:37,076 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:37,077 | ^ 2023-09-12T10:56:37,078 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:37,079 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:37,080 | ^~~~~~~~ 2023-09-12T10:56:37,248 In file included from include/openbabel/format.h:22, 2023-09-12T10:56:37,249 from include/openbabel/obconversion.h:37, 2023-09-12T10:56:37,249 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:56:37,250 include/openbabel/plugin.h: At global scope: 2023-09-12T10:56:37,251 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:37,252 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:37,253 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:37,253 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:56:37,254 from /usr/include/c++/12/vector:66, 2023-09-12T10:56:37,254 from include/openbabel/mol.h:35: 2023-09-12T10:56:37,255 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:37,255 131 | struct binary_function 2023-09-12T10:56:37,256 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:37,476 ./src/formats/abinitformat.cpp: In member function ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:56:37,476 ./src/formats/abinitformat.cpp:91:12: warning: variable ‘acell’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:56:37,477 91 | double acell[3]; // scale of lattice vectors 2023-09-12T10:56:37,477 | ^~~~~ 2023-09-12T10:56:39,856 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:56:39,856 /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]’: 2023-09-12T10:56:39,857 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:39,857 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:39,858 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:40,190 ./src/formats/abinitformat.cpp: In member function ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:56:40,191 ./src/formats/abinitformat.cpp:218:25: warning: ‘natom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:40,191 218 | for (int j = 0; j < natom; ++j) { 2023-09-12T10:56:40,192 | ~~^~~~~~~ 2023-09-12T10:56:40,193 ./src/formats/abinitformat.cpp:82:9: note: ‘natom’ was declared here 2023-09-12T10:56:40,194 82 | int natom; 2023-09-12T10:56:40,194 | ^~~~~ 2023-09-12T10:56:40,203 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:56:40,204 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, 2023-09-12T10:56:40,204 inlined from ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/abinitformat.cpp:129:27: 2023-09-12T10:56:40,205 /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 2023-09-12T10:56:40,206 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:40,207 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:40,207 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:56:40,208 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, 2023-09-12T10:56:40,209 inlined from ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/abinitformat.cpp:138:36: 2023-09-12T10:56:40,210 /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 2023-09-12T10:56:40,211 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:40,211 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:40,815 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:56:40,816 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/cceq8GcB.s 2023-09-12T10:56:40,820 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:41,047 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/ 2023-09-12T10:56:41,048 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/ 2023-09-12T10:56:41,048 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:56:41,050 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/formats/acesformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/acesformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:56:41,054 Using built-in specs. 2023-09-12T10:56:41,055 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:41,055 Target: arm-linux-gnueabihf 2023-09-12T10:56:41,056 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 2023-09-12T10:56:41,056 Thread model: posix 2023-09-12T10:56:41,057 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:41,058 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:41,058 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:56:41,059 /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/ccKqwyNf.s 2023-09-12T10:56:41,067 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:41,067 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 2023-09-12T10:56:41,068 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:41,069 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:41,069 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:41,070 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:41,071 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:41,071 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:41,072 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:41,073 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:41,073 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:41,074 #include "..." search starts here: 2023-09-12T10:56:41,075 #include <...> search starts here: 2023-09-12T10:56:41,076 /usr/include/eigen3 2023-09-12T10:56:41,077 include 2023-09-12T10:56:41,077 /usr/include/python3.11 2023-09-12T10:56:41,078 /usr/include/c++/12 2023-09-12T10:56:41,078 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:41,079 /usr/include/c++/12/backward 2023-09-12T10:56:41,080 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:41,080 /usr/local/include 2023-09-12T10:56:41,081 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:41,081 /usr/include 2023-09-12T10:56:41,082 End of search list. 2023-09-12T10:56:41,083 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:41,083 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:41,084 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:41,085 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:41,086 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:42,644 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:42,645 from include/openbabel/mol.h:43, 2023-09-12T10:56:42,646 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:56:42,647 from ./src/formats/acesformat.cpp:20: 2023-09-12T10:56:42,647 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:42,648 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:42,648 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:42,649 | ^ 2023-09-12T10:56:42,649 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:42,650 37 | # define UNUSED(x) x 2023-09-12T10:56:42,650 | ^ 2023-09-12T10:56:43,412 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:43,413 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:43,414 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:43,414 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:43,415 | ^ 2023-09-12T10:56:43,415 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:43,416 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:43,417 | ^~~~~~~~ 2023-09-12T10:56:43,418 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:43,418 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:43,419 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:43,420 | ^ 2023-09-12T10:56:43,420 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:43,421 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:43,422 | ^~~~~~~~ 2023-09-12T10:56:43,437 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:43,437 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:43,438 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:43,439 | ^ 2023-09-12T10:56:43,440 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:43,440 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:43,441 | ^~~~~~~~ 2023-09-12T10:56:43,443 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:43,444 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:43,444 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:43,446 | ^ 2023-09-12T10:56:43,446 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:43,447 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:43,447 | ^~~~~~~~ 2023-09-12T10:56:43,616 In file included from include/openbabel/format.h:22, 2023-09-12T10:56:43,616 from include/openbabel/obconversion.h:37, 2023-09-12T10:56:43,617 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:56:43,618 include/openbabel/plugin.h: At global scope: 2023-09-12T10:56:43,618 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:43,619 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:43,619 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:43,620 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:56:43,620 from /usr/include/c++/12/vector:66, 2023-09-12T10:56:43,621 from include/openbabel/mol.h:35: 2023-09-12T10:56:43,621 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:43,622 131 | struct binary_function 2023-09-12T10:56:43,623 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:46,617 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:56:46,617 /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]’: 2023-09-12T10:56:46,618 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:46,619 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:56:46,620 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:46,678 /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]’: 2023-09-12T10:56:46,679 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:56:47,502 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:47,503 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, 2023-09-12T10:56:47,503 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:182:37: 2023-09-12T10:56:47,504 /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 2023-09-12T10:56:47,505 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:47,506 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:47,506 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:47,507 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, 2023-09-12T10:56:47,508 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:184:37: 2023-09-12T10:56:47,509 /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 2023-09-12T10:56:47,509 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:47,510 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:47,510 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:56:47,511 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, 2023-09-12T10:56:47,512 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:198:37: 2023-09-12T10:56:47,512 /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 2023-09-12T10:56:47,513 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:47,513 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:47,514 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:56:47,514 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, 2023-09-12T10:56:47,515 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:200:37: 2023-09-12T10:56:47,515 /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 2023-09-12T10:56:47,516 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:47,517 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:47,518 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:56:47,519 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, 2023-09-12T10:56:47,519 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:202:37: 2023-09-12T10:56:47,520 /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 2023-09-12T10:56:47,521 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:47,522 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:47,522 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:56:47,523 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, 2023-09-12T10:56:47,524 inlined from ‘virtual bool OpenBabel::AcesOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/acesformat.cpp:225:39: 2023-09-12T10:56:47,525 /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 2023-09-12T10:56:47,525 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:56:47,526 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:56:48,567 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:56:48,567 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/ccKqwyNf.s 2023-09-12T10:56:48,572 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:48,904 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/ 2023-09-12T10:56:48,904 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/ 2023-09-12T10:56:48,905 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/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.' 2023-09-12T10:56:48,906 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 2023-09-12T10:56:48,910 Using built-in specs. 2023-09-12T10:56:48,911 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:48,912 Target: arm-linux-gnueabihf 2023-09-12T10:56:48,912 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 2023-09-12T10:56:48,913 Thread model: posix 2023-09-12T10:56:48,914 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:48,914 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:48,915 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:56:48,915 /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/ccd3aFUZ.s 2023-09-12T10:56:48,924 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:48,925 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:48,926 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:48,926 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:48,927 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:48,927 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:48,928 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:48,929 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:48,929 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:48,930 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:48,931 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:48,931 #include "..." search starts here: 2023-09-12T10:56:48,932 #include <...> search starts here: 2023-09-12T10:56:48,932 /usr/include/eigen3 2023-09-12T10:56:48,933 include 2023-09-12T10:56:48,933 /usr/include/python3.11 2023-09-12T10:56:48,934 /usr/include/c++/12 2023-09-12T10:56:48,934 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:48,935 /usr/include/c++/12/backward 2023-09-12T10:56:48,936 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:48,936 /usr/local/include 2023-09-12T10:56:48,937 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:48,937 /usr/include 2023-09-12T10:56:48,938 End of search list. 2023-09-12T10:56:48,938 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:48,939 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:48,940 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:48,941 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:48,944 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:50,525 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:50,526 from include/openbabel/mol.h:43, 2023-09-12T10:56:50,526 from ./src/formats/acrformat.cpp:23: 2023-09-12T10:56:50,527 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:50,528 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:50,528 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:50,529 | ^ 2023-09-12T10:56:50,529 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:50,530 37 | # define UNUSED(x) x 2023-09-12T10:56:50,530 | ^ 2023-09-12T10:56:51,294 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:51,295 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:51,295 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:51,296 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:51,296 | ^ 2023-09-12T10:56:51,297 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:51,298 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:51,299 | ^~~~~~~~ 2023-09-12T10:56:51,300 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:51,300 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:51,301 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:51,302 | ^ 2023-09-12T10:56:51,303 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:51,303 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:51,304 | ^~~~~~~~ 2023-09-12T10:56:51,318 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:51,319 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:51,320 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:51,320 | ^ 2023-09-12T10:56:51,321 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:51,322 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:51,322 | ^~~~~~~~ 2023-09-12T10:56:51,325 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:51,326 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:51,326 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:51,327 | ^ 2023-09-12T10:56:51,328 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:51,329 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:51,329 | ^~~~~~~~ 2023-09-12T10:56:51,499 In file included from include/openbabel/format.h:22, 2023-09-12T10:56:51,500 from include/openbabel/obconversion.h:37, 2023-09-12T10:56:51,500 from include/openbabel/obmolecformat.h:31, 2023-09-12T10:56:51,501 from ./src/formats/acrformat.cpp:24: 2023-09-12T10:56:51,501 include/openbabel/plugin.h: At global scope: 2023-09-12T10:56:51,502 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:51,502 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:51,503 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:51,504 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:56:51,504 from /usr/include/c++/12/vector:66, 2023-09-12T10:56:51,505 from include/openbabel/mol.h:35: 2023-09-12T10:56:51,505 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:51,506 131 | struct binary_function 2023-09-12T10:56:51,507 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:51,698 ./src/formats/acrformat.cpp: In member function ‘virtual int OpenBabel::ACRFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T10:56:51,699 ./src/formats/acrformat.cpp:67:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T10:56:51,700 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T10:56:51,701 | ~~~~^ 2023-09-12T10:56:51,701 ./src/formats/acrformat.cpp:67:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:56:51,702 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T10:56:51,703 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:56:51,705 ./src/formats/acrformat.cpp: In member function ‘virtual bool OpenBabel::ACRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:56:51,705 ./src/formats/acrformat.cpp:113:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:56:51,706 113 | } else if (sscanf(buf, "Number of Atoms in Crystal=%d\n", &tmp)) { 2023-09-12T10:56:51,707 | ~^ ~~~~ 2023-09-12T10:56:51,707 | | | 2023-09-12T10:56:51,708 | int* unsigned int* 2023-09-12T10:56:51,709 | %d 2023-09-12T10:56:51,709 ./src/formats/acrformat.cpp:120:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:56:51,710 120 | } else if (sscanf(buf, "Number of Links in Crystal=%d\n", &tmp)) { 2023-09-12T10:56:51,711 | ~^ ~~~~ 2023-09-12T10:56:51,712 | | | 2023-09-12T10:56:51,712 | int* unsigned int* 2023-09-12T10:56:51,713 | %d 2023-09-12T10:56:53,565 ./src/formats/acrformat.cpp:137:40: warning: ‘scale’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:53,565 137 | X = atof((char*)vs[6].c_str())/scale; 2023-09-12T10:56:53,566 | ^~~~~ 2023-09-12T10:56:53,566 ./src/formats/acrformat.cpp:93:11: note: ‘scale’ was declared here 2023-09-12T10:56:53,567 93 | float scale, dtmp; 2023-09-12T10:56:53,568 | ^~~~~ 2023-09-12T10:56:53,568 ./src/formats/acrformat.cpp:159:5: warning: ‘bonds’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:53,569 159 | if ( pmol->NumBonds() != bonds ) { 2023-09-12T10:56:53,569 | ^~ 2023-09-12T10:56:53,570 ./src/formats/acrformat.cpp:92:25: note: ‘bonds’ was declared here 2023-09-12T10:56:53,570 92 | unsigned int atoms, bonds, tmp; 2023-09-12T10:56:53,571 | ^~~~~ 2023-09-12T10:56:53,572 ./src/formats/acrformat.cpp:163:12: warning: ‘atoms’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:56:53,572 163 | } else if ( pmol->NumAtoms() != atoms ) { 2023-09-12T10:56:53,573 | ^~ 2023-09-12T10:56:53,573 ./src/formats/acrformat.cpp:92:18: note: ‘atoms’ was declared here 2023-09-12T10:56:53,574 92 | unsigned int atoms, bonds, tmp; 2023-09-12T10:56:53,575 | ^~~~~ 2023-09-12T10:56:54,434 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:56:54,434 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/ccd3aFUZ.s 2023-09-12T10:56:54,439 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:56:54,631 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/ 2023-09-12T10:56:54,631 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/ 2023-09-12T10:56:54,632 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:56:54,633 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/adfformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/adfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:56:54,637 Using built-in specs. 2023-09-12T10:56:54,638 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:56:54,638 Target: arm-linux-gnueabihf 2023-09-12T10:56:54,639 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 2023-09-12T10:56:54,640 Thread model: posix 2023-09-12T10:56:54,640 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:56:54,641 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:56:54,641 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/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/' 2023-09-12T10:56:54,642 /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/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/ccDCiFAu.s 2023-09-12T10:56:54,650 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:54,650 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:54,651 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:54,652 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:54,653 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:56:54,653 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:56:54,654 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:56:54,654 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:56:54,655 ignoring duplicate directory "/usr/include/" 2023-09-12T10:56:54,656 as it is a non-system directory that duplicates a system directory 2023-09-12T10:56:54,656 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:56:54,657 #include "..." search starts here: 2023-09-12T10:56:54,658 #include <...> search starts here: 2023-09-12T10:56:54,658 /usr/include/eigen3 2023-09-12T10:56:54,659 include 2023-09-12T10:56:54,660 /usr/include/python3.11 2023-09-12T10:56:54,660 /usr/include/c++/12 2023-09-12T10:56:54,661 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:56:54,661 /usr/include/c++/12/backward 2023-09-12T10:56:54,662 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:56:54,662 /usr/local/include 2023-09-12T10:56:54,663 /usr/include/arm-linux-gnueabihf 2023-09-12T10:56:54,663 /usr/include 2023-09-12T10:56:54,663 End of search list. 2023-09-12T10:56:54,664 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:56:54,664 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:56:54,665 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:56:54,666 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:56:54,668 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:56:56,203 In file included from include/openbabel/format.h:22, 2023-09-12T10:56:56,204 from include/openbabel/obconversion.h:37, 2023-09-12T10:56:56,205 from ./src/formats/adfformat.cpp:34: 2023-09-12T10:56:56,205 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:56:56,206 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:56:56,206 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:56,207 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:56:56,207 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:56:56,208 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:56:56,209 from /usr/include/c++/12/ios:42, 2023-09-12T10:56:56,210 from /usr/include/c++/12/istream:38, 2023-09-12T10:56:56,210 from /usr/include/c++/12/fstream:38, 2023-09-12T10:56:56,211 from ./src/formats/adfformat.cpp:28: 2023-09-12T10:56:56,212 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:56:56,213 131 | struct binary_function 2023-09-12T10:56:56,213 | ^~~~~~~~~~~~~~~ 2023-09-12T10:56:56,431 In file included from include/openbabel/atom.h:33, 2023-09-12T10:56:56,432 from include/openbabel/mol.h:43, 2023-09-12T10:56:56,433 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:56:56,434 from ./src/formats/adfformat.cpp:35: 2023-09-12T10:56:56,434 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:56:56,435 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:56:56,436 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:56:56,437 | ^ 2023-09-12T10:56:56,437 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:56:56,438 37 | # define UNUSED(x) x 2023-09-12T10:56:56,439 | ^ 2023-09-12T10:56:57,102 In file included from include/openbabel/mol.h:52: 2023-09-12T10:56:57,103 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:57,104 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:57,104 862 | {return new OBVibrationData(*this);} 2023-09-12T10:56:57,105 | ^ 2023-09-12T10:56:57,106 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:56:57,107 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:56:57,108 | ^~~~~~~~ 2023-09-12T10:56:57,108 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:57,109 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:57,110 907 | {return new OBDOSData(*this);} 2023-09-12T10:56:57,110 | ^ 2023-09-12T10:56:57,111 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:56:57,111 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:56:57,112 | ^~~~~~~~ 2023-09-12T10:56:57,128 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:57,129 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:57,129 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:56:57,130 | ^ 2023-09-12T10:56:57,131 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:56:57,131 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:56:57,132 | ^~~~~~~~ 2023-09-12T10:56:57,134 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:56:57,135 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:56:57,136 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:56:57,137 | ^ 2023-09-12T10:56:57,138 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:56:57,138 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:56:57,139 | ^~~~~~~~ 2023-09-12T10:56:57,402 ./src/formats/adfformat.cpp: In member function ‘virtual bool OpenBabel::ADFInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:56:57,403 ./src/formats/adfformat.cpp:274:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2023-09-12T10:56:57,403 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2023-09-12T10:56:57,404 | ~~~~~~~~^~~ 2023-09-12T10:56:57,405 ./src/formats/adfformat.cpp:274:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:56:57,406 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2023-09-12T10:56:57,407 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:56:57,416 ./src/formats/adfformat.cpp: In member function ‘virtual int OpenBabel::OBT41Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T10:56:57,417 ./src/formats/adfformat.cpp:400:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T10:56:57,418 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2023-09-12T10:56:57,418 | ~~~~^ 2023-09-12T10:56:57,419 ./src/formats/adfformat.cpp:400:51: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:56:57,420 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2023-09-12T10:56:57,420 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:56:57,421 ./src/formats/adfformat.cpp: In member function ‘void OpenBabel::OBT41Format::AddSCFGrids(std::istream&, OpenBabel::OBGridData&)’: 2023-09-12T10:56:57,421 ./src/formats/adfformat.cpp:448:32: warning: unused parameter ‘is’ [-Wunused-parameter] 2023-09-12T10:56:57,422 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2023-09-12T10:56:57,422 | ~~~~~~~~~^~ 2023-09-12T10:56:57,423 ./src/formats/adfformat.cpp:448:48: warning: unused parameter ‘t41’ [-Wunused-parameter] 2023-09-12T10:56:57,424 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2023-09-12T10:56:57,424 | ~~~~~~~~~~~~^~~ 2023-09-12T10:56:57,425 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadBinary(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:56:57,426 ./src/formats/adfformat.cpp:533:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2023-09-12T10:56:57,426 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2023-09-12T10:56:57,427 | ~~~~~~~~^~~ 2023-09-12T10:56:57,428 ./src/formats/adfformat.cpp:533:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:56:57,429 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2023-09-12T10:56:57,429 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:56:57,433 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadASCII(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:56:57,434 ./src/formats/adfformat.cpp:590:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:56:57,435 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,436 | ^~~~~ 2023-09-12T10:56:57,436 ./src/formats/adfformat.cpp:590:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:56:57,437 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,438 | ^~~~ 2023-09-12T10:56:57,439 ./src/formats/adfformat.cpp:603:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:56:57,440 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,441 | ^~~~~ 2023-09-12T10:56:57,441 ./src/formats/adfformat.cpp:603:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:56:57,442 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,443 | ^~~~ 2023-09-12T10:56:57,458 ./src/formats/adfformat.cpp:625:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:56:57,459 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,460 | ^~~~~ 2023-09-12T10:56:57,461 ./src/formats/adfformat.cpp:625:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:56:57,462 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,463 | ^~~~ 2023-09-12T10:56:57,466 ./src/formats/adfformat.cpp:640:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:56:57,467 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,467 | ^~~~~ 2023-09-12T10:56:57,468 ./src/formats/adfformat.cpp:640:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:56:57,469 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,469 | ^~~~ 2023-09-12T10:56:57,471 ./src/formats/adfformat.cpp:655:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T10:56:57,472 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,472 | ^~~~~ 2023-09-12T10:56:57,473 ./src/formats/adfformat.cpp:655:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2023-09-12T10:56:57,474 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2023-09-12T10:56:57,474 | ^~~~ 2023-09-12T10:57:03,413 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:57:03,413 from ./src/formats/adfformat.cpp:30: 2023-09-12T10:57:03,414 /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]’: 2023-09-12T10:57:03,414 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:03,415 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:03,416 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:03,912 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::OBT41Format::AtomData}; _Tp = OpenBabel::OBT41Format::AtomData; _Alloc = std::allocator]’, 2023-09-12T10:57:03,913 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, 2023-09-12T10:57:03,914 inlined from ‘bool OpenBabel::OBT41Format::ReadASCII(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/adfformat.cpp:616:26: 2023-09-12T10:57:03,914 /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 2023-09-12T10:57:03,915 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:03,916 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:05,265 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:05,266 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/ccDCiFAu.s 2023-09-12T10:57:05,270 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:05,886 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/ 2023-09-12T10:57:05,887 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/ 2023-09-12T10:57:05,887 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:57:05,890 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 2023-09-12T10:57:05,894 Using built-in specs. 2023-09-12T10:57:05,895 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:05,895 Target: arm-linux-gnueabihf 2023-09-12T10:57:05,896 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 2023-09-12T10:57:05,896 Thread model: posix 2023-09-12T10:57:05,897 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:05,897 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:05,898 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/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/' 2023-09-12T10:57:05,899 /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/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/ccVKNUch.s 2023-09-12T10:57:05,907 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:05,908 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 2023-09-12T10:57:05,909 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:05,909 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:05,910 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:05,910 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:05,911 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:05,911 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:05,912 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:05,912 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:05,913 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:05,913 #include "..." search starts here: 2023-09-12T10:57:05,913 #include <...> search starts here: 2023-09-12T10:57:05,914 /usr/include/eigen3 2023-09-12T10:57:05,914 include 2023-09-12T10:57:05,915 /usr/include/python3.11 2023-09-12T10:57:05,916 /usr/include/c++/12 2023-09-12T10:57:05,916 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:05,917 /usr/include/c++/12/backward 2023-09-12T10:57:05,917 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:05,918 /usr/local/include 2023-09-12T10:57:05,919 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:05,919 /usr/include 2023-09-12T10:57:05,920 End of search list. 2023-09-12T10:57:05,920 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:05,921 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 2023-09-12T10:57:05,923 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:05,923 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:05,927 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:07,497 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:07,498 from include/openbabel/mol.h:43, 2023-09-12T10:57:07,499 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:07,499 from ./src/formats/alchemyformat.cpp:17: 2023-09-12T10:57:07,500 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:07,500 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:07,501 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:07,502 | ^ 2023-09-12T10:57:07,502 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:07,503 37 | # define UNUSED(x) x 2023-09-12T10:57:07,504 | ^ 2023-09-12T10:57:08,273 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:08,273 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:08,274 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:08,275 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:08,276 | ^ 2023-09-12T10:57:08,276 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:08,277 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:08,277 | ^~~~~~~~ 2023-09-12T10:57:08,280 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:08,281 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:08,281 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:08,282 | ^ 2023-09-12T10:57:08,283 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:08,283 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:08,284 | ^~~~~~~~ 2023-09-12T10:57:08,300 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:08,301 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:08,302 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:08,302 | ^ 2023-09-12T10:57:08,303 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:08,304 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:08,305 | ^~~~~~~~ 2023-09-12T10:57:08,308 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:08,309 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:08,310 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:08,310 | ^ 2023-09-12T10:57:08,311 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:08,312 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:08,312 | ^~~~~~~~ 2023-09-12T10:57:08,482 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:08,483 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:08,484 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:08,484 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:08,485 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:08,486 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:08,486 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:08,488 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:08,488 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:08,489 from include/openbabel/mol.h:35: 2023-09-12T10:57:08,489 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:08,490 131 | struct binary_function 2023-09-12T10:57:08,490 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:11,390 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:11,391 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/ccVKNUch.s 2023-09-12T10:57:11,395 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:11,569 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/ 2023-09-12T10:57:11,570 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/ 2023-09-12T10:57:11,570 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/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.' 2023-09-12T10:57:11,572 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 2023-09-12T10:57:11,575 Using built-in specs. 2023-09-12T10:57:11,576 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:11,577 Target: arm-linux-gnueabihf 2023-09-12T10:57:11,577 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 2023-09-12T10:57:11,578 Thread model: posix 2023-09-12T10:57:11,579 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:11,579 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:11,580 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/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/' 2023-09-12T10:57:11,580 /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/ccDQPfG5.s 2023-09-12T10:57:11,589 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:11,589 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 2023-09-12T10:57:11,590 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:11,591 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:11,591 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:11,592 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:11,592 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:11,593 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:11,594 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:11,594 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:11,595 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:11,595 #include "..." search starts here: 2023-09-12T10:57:11,596 #include <...> search starts here: 2023-09-12T10:57:11,596 /usr/include/eigen3 2023-09-12T10:57:11,597 include 2023-09-12T10:57:11,597 /usr/include/python3.11 2023-09-12T10:57:11,598 /usr/include/c++/12 2023-09-12T10:57:11,599 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:11,599 /usr/include/c++/12/backward 2023-09-12T10:57:11,600 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:11,600 /usr/local/include 2023-09-12T10:57:11,601 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:11,601 /usr/include 2023-09-12T10:57:11,602 End of search list. 2023-09-12T10:57:11,602 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:11,603 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:11,604 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:11,605 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:11,608 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:13,188 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:13,188 from include/openbabel/mol.h:43, 2023-09-12T10:57:13,189 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:13,190 from ./src/formats/amberformat.cpp:17: 2023-09-12T10:57:13,190 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:13,191 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:13,191 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:13,192 | ^ 2023-09-12T10:57:13,192 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:13,193 37 | # define UNUSED(x) x 2023-09-12T10:57:13,193 | ^ 2023-09-12T10:57:13,954 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:13,955 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,955 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,956 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:13,957 | ^ 2023-09-12T10:57:13,957 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:13,958 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:13,958 | ^~~~~~~~ 2023-09-12T10:57:13,960 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,960 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,961 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:13,962 | ^ 2023-09-12T10:57:13,962 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:13,963 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:13,964 | ^~~~~~~~ 2023-09-12T10:57:13,979 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,980 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,981 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:13,981 | ^ 2023-09-12T10:57:13,982 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:13,983 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:13,983 | ^~~~~~~~ 2023-09-12T10:57:13,986 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:13,987 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:13,988 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:13,989 | ^ 2023-09-12T10:57:13,989 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:13,990 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:13,990 | ^~~~~~~~ 2023-09-12T10:57:14,159 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:14,160 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:14,160 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:14,161 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:14,161 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:14,162 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:14,162 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:14,163 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:14,163 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:14,164 from include/openbabel/mol.h:35: 2023-09-12T10:57:14,165 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:14,165 131 | struct binary_function 2023-09-12T10:57:14,166 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:16,877 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/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/' 2023-09-12T10:57:16,878 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/formats/amberformat.o /tmp/ccDQPfG5.s 2023-09-12T10:57:16,882 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:17,038 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/ 2023-09-12T10:57:17,039 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/ 2023-09-12T10:57:17,039 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:57:17,040 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 2023-09-12T10:57:17,044 Using built-in specs. 2023-09-12T10:57:17,045 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:17,045 Target: arm-linux-gnueabihf 2023-09-12T10:57:17,046 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 2023-09-12T10:57:17,046 Thread model: posix 2023-09-12T10:57:17,047 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:17,047 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:17,048 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:17,048 /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/cc0wUC3O.s 2023-09-12T10:57:17,057 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:17,057 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:17,058 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:17,059 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:17,060 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:17,060 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:17,061 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:17,061 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:17,062 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:17,063 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:17,063 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:17,064 #include "..." search starts here: 2023-09-12T10:57:17,065 #include <...> search starts here: 2023-09-12T10:57:17,065 /usr/include/eigen3 2023-09-12T10:57:17,066 include 2023-09-12T10:57:17,066 /usr/include/python3.11 2023-09-12T10:57:17,066 /usr/include/c++/12 2023-09-12T10:57:17,067 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:17,067 /usr/include/c++/12/backward 2023-09-12T10:57:17,068 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:17,068 /usr/local/include 2023-09-12T10:57:17,068 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:17,069 /usr/include 2023-09-12T10:57:17,069 End of search list. 2023-09-12T10:57:17,070 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:17,070 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:17,071 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:17,071 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:17,075 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:18,636 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:18,637 from include/openbabel/mol.h:43, 2023-09-12T10:57:18,637 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:18,638 from ./src/formats/aoforceformat.cpp:17: 2023-09-12T10:57:18,638 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:18,639 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:18,640 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:18,640 | ^ 2023-09-12T10:57:18,641 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:18,642 37 | # define UNUSED(x) x 2023-09-12T10:57:18,642 | ^ 2023-09-12T10:57:19,404 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:19,405 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:19,405 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:19,406 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:19,407 | ^ 2023-09-12T10:57:19,408 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:19,408 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:19,409 | ^~~~~~~~ 2023-09-12T10:57:19,410 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:19,410 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:19,411 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:19,412 | ^ 2023-09-12T10:57:19,413 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:19,413 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:19,414 | ^~~~~~~~ 2023-09-12T10:57:19,428 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:19,429 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:19,430 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:19,430 | ^ 2023-09-12T10:57:19,431 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:19,431 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:19,432 | ^~~~~~~~ 2023-09-12T10:57:19,434 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:19,435 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:19,436 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:19,436 | ^ 2023-09-12T10:57:19,437 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:19,437 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:19,438 | ^~~~~~~~ 2023-09-12T10:57:19,606 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:19,607 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:19,608 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:19,609 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:19,609 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:19,610 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:19,611 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:19,612 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:19,612 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:19,613 from include/openbabel/mol.h:35: 2023-09-12T10:57:19,614 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:19,614 131 | struct binary_function 2023-09-12T10:57:19,615 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:22,668 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:57:22,669 /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]’: 2023-09-12T10:57:22,670 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:22,670 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:57:22,671 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:22,730 /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]’: 2023-09-12T10:57:22,730 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:57:23,053 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:23,054 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, 2023-09-12T10:57:23,055 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:82:30: 2023-09-12T10:57:23,056 /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 2023-09-12T10:57:23,056 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:23,057 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:23,057 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:23,058 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, 2023-09-12T10:57:23,058 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:94:30: 2023-09-12T10:57:23,059 /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 2023-09-12T10:57:23,060 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:23,060 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:23,061 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:23,062 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, 2023-09-12T10:57:23,063 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:108:23: 2023-09-12T10:57:23,063 /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 2023-09-12T10:57:23,064 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:23,065 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:23,065 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:23,066 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, 2023-09-12T10:57:23,067 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:115:23: 2023-09-12T10:57:23,067 /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 2023-09-12T10:57:23,068 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:23,069 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:23,070 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:57:23,071 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, 2023-09-12T10:57:23,072 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:122:23: 2023-09-12T10:57:23,072 /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 2023-09-12T10:57:23,073 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:23,073 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:23,074 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:57:23,074 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, 2023-09-12T10:57:23,075 inlined from ‘virtual bool OpenBabel::AoforceFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/aoforceformat.cpp:134:28: 2023-09-12T10:57:23,076 /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 2023-09-12T10:57:23,076 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:57:23,077 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:57:24,061 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:24,062 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/cc0wUC3O.s 2023-09-12T10:57:24,070 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:24,377 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/ 2023-09-12T10:57:24,378 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/ 2023-09-12T10:57:24,379 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/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.' 2023-09-12T10:57:24,380 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/formats/asciiformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/asciiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:57:24,384 Using built-in specs. 2023-09-12T10:57:24,385 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:24,386 Target: arm-linux-gnueabihf 2023-09-12T10:57:24,386 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 2023-09-12T10:57:24,386 Thread model: posix 2023-09-12T10:57:24,387 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:24,387 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:24,388 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/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/' 2023-09-12T10:57:24,388 /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/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/ccVVHxaV.s 2023-09-12T10:57:24,397 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:24,398 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 2023-09-12T10:57:24,399 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:24,400 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:24,400 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:24,401 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:24,401 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:24,402 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:24,403 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:24,403 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:24,404 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:24,405 #include "..." search starts here: 2023-09-12T10:57:24,405 #include <...> search starts here: 2023-09-12T10:57:24,406 /usr/include/eigen3 2023-09-12T10:57:24,406 include 2023-09-12T10:57:24,407 /usr/include/python3.11 2023-09-12T10:57:24,407 /usr/include/c++/12 2023-09-12T10:57:24,407 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:24,408 /usr/include/c++/12/backward 2023-09-12T10:57:24,408 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:24,409 /usr/local/include 2023-09-12T10:57:24,409 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:24,409 /usr/include 2023-09-12T10:57:24,410 End of search list. 2023-09-12T10:57:24,410 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:24,411 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 2023-09-12T10:57:24,412 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:24,412 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:24,418 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:25,990 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:25,991 from include/openbabel/mol.h:43, 2023-09-12T10:57:25,991 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:25,992 from ./src/formats/asciiformat.cpp:19: 2023-09-12T10:57:25,992 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:25,993 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:25,994 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:25,994 | ^ 2023-09-12T10:57:25,995 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:25,996 37 | # define UNUSED(x) x 2023-09-12T10:57:25,996 | ^ 2023-09-12T10:57:26,760 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:26,760 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:26,761 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:26,762 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:26,762 | ^ 2023-09-12T10:57:26,763 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:26,764 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:26,764 | ^~~~~~~~ 2023-09-12T10:57:26,766 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:26,767 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:26,767 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:26,768 | ^ 2023-09-12T10:57:26,769 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:26,770 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:26,771 | ^~~~~~~~ 2023-09-12T10:57:26,787 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:26,787 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:26,788 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:26,788 | ^ 2023-09-12T10:57:26,789 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:26,789 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:26,790 | ^~~~~~~~ 2023-09-12T10:57:26,793 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:26,793 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:26,794 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:26,794 | ^ 2023-09-12T10:57:26,795 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:26,796 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:26,796 | ^~~~~~~~ 2023-09-12T10:57:26,966 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:26,966 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:26,967 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:26,968 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:26,969 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:26,969 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:26,970 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:26,971 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:26,972 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:26,972 from include/openbabel/mol.h:35: 2023-09-12T10:57:26,973 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:26,973 131 | struct binary_function 2023-09-12T10:57:26,974 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:27,200 In file included from ./src/formats/asciiformat.cpp:22: 2023-09-12T10:57:27,201 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2023-09-12T10:57:27,201 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T10:57:27,202 34 | void SetFontFamily(const std::string &fontFamily) {} 2023-09-12T10:57:27,203 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:57:29,775 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/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/' 2023-09-12T10:57:29,776 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/asciiformat.o /tmp/ccVVHxaV.s 2023-09-12T10:57:29,780 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:29,965 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/ 2023-09-12T10:57:29,965 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/ 2023-09-12T10:57:29,966 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:57:29,967 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/balstformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/balstformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:57:29,972 Using built-in specs. 2023-09-12T10:57:29,972 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:29,973 Target: arm-linux-gnueabihf 2023-09-12T10:57:29,974 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 2023-09-12T10:57:29,974 Thread model: posix 2023-09-12T10:57:29,975 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:29,975 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:29,976 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:29,976 /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/ccOjyDqX.s 2023-09-12T10:57:29,985 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:29,986 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:29,987 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:29,987 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:29,987 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:29,988 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:29,988 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:29,989 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:29,989 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:29,990 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:29,990 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:29,991 #include "..." search starts here: 2023-09-12T10:57:29,991 #include <...> search starts here: 2023-09-12T10:57:29,992 /usr/include/eigen3 2023-09-12T10:57:29,992 include 2023-09-12T10:57:29,993 /usr/include/python3.11 2023-09-12T10:57:29,994 /usr/include/c++/12 2023-09-12T10:57:29,994 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:29,995 /usr/include/c++/12/backward 2023-09-12T10:57:29,995 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:29,996 /usr/local/include 2023-09-12T10:57:29,997 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:29,997 /usr/include 2023-09-12T10:57:29,998 End of search list. 2023-09-12T10:57:29,999 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:29,999 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 2023-09-12T10:57:30,001 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:30,001 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:30,004 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:31,571 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:31,571 from include/openbabel/mol.h:43, 2023-09-12T10:57:31,572 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:31,573 from ./src/formats/balstformat.cpp:17: 2023-09-12T10:57:31,573 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:31,574 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:31,575 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:31,575 | ^ 2023-09-12T10:57:31,576 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:31,577 37 | # define UNUSED(x) x 2023-09-12T10:57:31,577 | ^ 2023-09-12T10:57:32,341 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:32,341 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:32,342 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:32,342 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:32,343 | ^ 2023-09-12T10:57:32,343 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:32,344 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:32,344 | ^~~~~~~~ 2023-09-12T10:57:32,346 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:32,346 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:32,347 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:32,348 | ^ 2023-09-12T10:57:32,348 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:32,349 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:32,350 | ^~~~~~~~ 2023-09-12T10:57:32,365 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:32,365 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:32,366 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:32,367 | ^ 2023-09-12T10:57:32,367 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:32,368 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:32,369 | ^~~~~~~~ 2023-09-12T10:57:32,371 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:32,372 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:32,372 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:32,373 | ^ 2023-09-12T10:57:32,374 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:32,374 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:32,375 | ^~~~~~~~ 2023-09-12T10:57:32,544 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:32,545 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:32,546 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:32,547 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:32,547 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:32,548 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:32,548 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:32,549 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:32,549 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:32,550 from include/openbabel/mol.h:35: 2023-09-12T10:57:32,550 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:32,551 131 | struct binary_function 2023-09-12T10:57:32,551 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:35,305 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/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/' 2023-09-12T10:57:35,305 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/ccOjyDqX.s 2023-09-12T10:57:35,310 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:35,471 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/ 2023-09-12T10:57:35,471 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/ 2023-09-12T10:57:35,472 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:57:35,472 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 2023-09-12T10:57:35,477 Using built-in specs. 2023-09-12T10:57:35,478 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:35,478 Target: arm-linux-gnueabihf 2023-09-12T10:57:35,479 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 2023-09-12T10:57:35,482 Thread model: posix 2023-09-12T10:57:35,483 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:35,483 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:35,484 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:35,484 /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/cchsK4JK.s 2023-09-12T10:57:35,493 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:35,494 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:35,495 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:35,495 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:35,496 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:35,496 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:35,497 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:35,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:35,498 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:35,499 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:35,500 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:35,500 #include "..." search starts here: 2023-09-12T10:57:35,501 #include <...> search starts here: 2023-09-12T10:57:35,501 /usr/include/eigen3 2023-09-12T10:57:35,502 include 2023-09-12T10:57:35,502 /usr/include/python3.11 2023-09-12T10:57:35,503 /usr/include/c++/12 2023-09-12T10:57:35,503 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:35,504 /usr/include/c++/12/backward 2023-09-12T10:57:35,504 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:35,505 /usr/local/include 2023-09-12T10:57:35,506 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:35,506 /usr/include 2023-09-12T10:57:35,507 End of search list. 2023-09-12T10:57:35,507 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:35,508 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:35,509 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:35,510 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:35,513 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:37,092 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:37,093 from include/openbabel/mol.h:43, 2023-09-12T10:57:37,093 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:37,094 from ./src/formats/bgfformat.cpp:17: 2023-09-12T10:57:37,094 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:37,095 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:37,095 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:37,096 | ^ 2023-09-12T10:57:37,096 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:37,097 37 | # define UNUSED(x) x 2023-09-12T10:57:37,097 | ^ 2023-09-12T10:57:37,860 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:37,860 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:37,861 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:37,862 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:37,862 | ^ 2023-09-12T10:57:37,863 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:37,864 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:37,865 | ^~~~~~~~ 2023-09-12T10:57:37,866 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:37,866 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:37,867 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:37,868 | ^ 2023-09-12T10:57:37,869 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:37,869 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:37,870 | ^~~~~~~~ 2023-09-12T10:57:37,885 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:37,886 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:37,886 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:37,887 | ^ 2023-09-12T10:57:37,888 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:37,889 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:37,889 | ^~~~~~~~ 2023-09-12T10:57:37,892 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:37,893 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:37,894 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:37,894 | ^ 2023-09-12T10:57:37,895 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:37,895 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:37,896 | ^~~~~~~~ 2023-09-12T10:57:38,065 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:38,065 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:38,066 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:38,067 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:38,067 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:38,068 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:38,068 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:38,069 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:38,070 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:38,070 from include/openbabel/mol.h:35: 2023-09-12T10:57:38,071 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:38,071 131 | struct binary_function 2023-09-12T10:57:38,072 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:41,719 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:41,720 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/cchsK4JK.s 2023-09-12T10:57:41,726 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:41,968 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/ 2023-09-12T10:57:41,968 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/ 2023-09-12T10:57:41,969 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/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.' 2023-09-12T10:57:41,970 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 2023-09-12T10:57:41,974 Using built-in specs. 2023-09-12T10:57:41,975 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:41,975 Target: arm-linux-gnueabihf 2023-09-12T10:57:41,976 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 2023-09-12T10:57:41,976 Thread model: posix 2023-09-12T10:57:41,977 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:41,977 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:41,978 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/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/' 2023-09-12T10:57:41,978 /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/ccvJGpej.s 2023-09-12T10:57:41,987 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:41,988 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:41,989 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:41,989 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:41,990 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:41,990 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:41,991 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:41,992 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:41,992 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:41,993 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:41,994 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:41,994 #include "..." search starts here: 2023-09-12T10:57:41,995 #include <...> search starts here: 2023-09-12T10:57:41,995 /usr/include/eigen3 2023-09-12T10:57:41,995 include 2023-09-12T10:57:41,996 /usr/include/python3.11 2023-09-12T10:57:41,996 /usr/include/c++/12 2023-09-12T10:57:41,997 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:41,997 /usr/include/c++/12/backward 2023-09-12T10:57:41,998 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:41,998 /usr/local/include 2023-09-12T10:57:41,998 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:41,999 /usr/include 2023-09-12T10:57:42,000 End of search list. 2023-09-12T10:57:42,000 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:42,000 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:42,001 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:42,002 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:42,005 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:43,564 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:43,564 from include/openbabel/mol.h:43, 2023-09-12T10:57:43,565 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:43,566 from ./src/formats/boxformat.cpp:17: 2023-09-12T10:57:43,566 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:43,567 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:43,568 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:43,569 | ^ 2023-09-12T10:57:43,570 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:43,570 37 | # define UNUSED(x) x 2023-09-12T10:57:43,571 | ^ 2023-09-12T10:57:44,330 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:44,331 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:44,332 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:44,332 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:44,333 | ^ 2023-09-12T10:57:44,334 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:44,334 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:44,335 | ^~~~~~~~ 2023-09-12T10:57:44,336 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:44,336 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:44,337 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:44,338 | ^ 2023-09-12T10:57:44,339 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:44,340 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:44,340 | ^~~~~~~~ 2023-09-12T10:57:44,355 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:44,355 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:44,356 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:44,356 | ^ 2023-09-12T10:57:44,357 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:44,357 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:44,358 | ^~~~~~~~ 2023-09-12T10:57:44,361 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:44,361 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:44,362 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:44,363 | ^ 2023-09-12T10:57:44,363 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:44,364 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:44,365 | ^~~~~~~~ 2023-09-12T10:57:44,533 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:44,534 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:44,534 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:44,535 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:44,536 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:44,536 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:44,537 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:44,538 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:44,538 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:44,539 from include/openbabel/mol.h:35: 2023-09-12T10:57:44,540 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:44,540 131 | struct binary_function 2023-09-12T10:57:44,541 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:47,552 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:47,553 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/ccvJGpej.s 2023-09-12T10:57:47,557 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:47,749 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/ 2023-09-12T10:57:47,750 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/ 2023-09-12T10:57:47,750 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:57:47,752 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 2023-09-12T10:57:47,756 Using built-in specs. 2023-09-12T10:57:47,757 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:47,757 Target: arm-linux-gnueabihf 2023-09-12T10:57:47,758 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 2023-09-12T10:57:47,758 Thread model: posix 2023-09-12T10:57:47,759 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:47,759 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:47,760 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/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/' 2023-09-12T10:57:47,761 /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/ccbnBfNT.s 2023-09-12T10:57:47,769 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:47,770 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:47,771 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:47,771 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:47,772 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:47,772 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:47,773 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:47,773 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:47,774 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:47,774 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:47,774 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:47,775 #include "..." search starts here: 2023-09-12T10:57:47,776 #include <...> search starts here: 2023-09-12T10:57:47,776 /usr/include/eigen3 2023-09-12T10:57:47,777 include 2023-09-12T10:57:47,777 /usr/include/python3.11 2023-09-12T10:57:47,778 /usr/include/c++/12 2023-09-12T10:57:47,779 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:47,779 /usr/include/c++/12/backward 2023-09-12T10:57:47,780 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:47,781 /usr/local/include 2023-09-12T10:57:47,782 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:47,782 /usr/include 2023-09-12T10:57:47,783 End of search list. 2023-09-12T10:57:47,784 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:47,784 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:47,786 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:47,786 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:47,787 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:49,345 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:49,346 from include/openbabel/mol.h:43, 2023-09-12T10:57:49,346 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:49,347 from ./src/formats/cacaoformat.cpp:17: 2023-09-12T10:57:49,348 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:49,348 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:49,349 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:49,350 | ^ 2023-09-12T10:57:49,350 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:49,351 37 | # define UNUSED(x) x 2023-09-12T10:57:49,352 | ^ 2023-09-12T10:57:50,113 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:50,113 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:50,114 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:50,115 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:50,116 | ^ 2023-09-12T10:57:50,116 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:50,117 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:50,117 | ^~~~~~~~ 2023-09-12T10:57:50,118 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:50,118 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:50,119 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:50,120 | ^ 2023-09-12T10:57:50,120 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:50,121 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:50,121 | ^~~~~~~~ 2023-09-12T10:57:50,137 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:50,137 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:50,138 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:50,139 | ^ 2023-09-12T10:57:50,140 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:50,140 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:50,141 | ^~~~~~~~ 2023-09-12T10:57:50,143 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:50,144 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:50,145 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:50,145 | ^ 2023-09-12T10:57:50,146 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:50,147 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:50,148 | ^~~~~~~~ 2023-09-12T10:57:50,316 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:50,317 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:50,318 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:50,319 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:50,319 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:50,320 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:50,321 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:50,322 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:50,322 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:50,323 from include/openbabel/mol.h:35: 2023-09-12T10:57:50,323 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:50,324 131 | struct binary_function 2023-09-12T10:57:50,324 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:53,633 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/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/' 2023-09-12T10:57:53,634 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/ccbnBfNT.s 2023-09-12T10:57:53,638 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:53,844 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/ 2023-09-12T10:57:53,844 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/ 2023-09-12T10:57:53,845 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:57:53,846 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 2023-09-12T10:57:53,850 Using built-in specs. 2023-09-12T10:57:53,851 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:53,852 Target: arm-linux-gnueabihf 2023-09-12T10:57:53,852 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 2023-09-12T10:57:53,853 Thread model: posix 2023-09-12T10:57:53,853 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:53,854 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:53,854 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:53,855 /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/ccOfref3.s 2023-09-12T10:57:53,863 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:53,864 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 2023-09-12T10:57:53,865 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:53,865 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:53,866 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:53,866 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:53,867 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:53,868 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:53,868 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:53,869 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:53,870 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:53,870 #include "..." search starts here: 2023-09-12T10:57:53,871 #include <...> search starts here: 2023-09-12T10:57:53,871 /usr/include/eigen3 2023-09-12T10:57:53,872 include 2023-09-12T10:57:53,872 /usr/include/python3.11 2023-09-12T10:57:53,873 /usr/include/c++/12 2023-09-12T10:57:53,874 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:53,874 /usr/include/c++/12/backward 2023-09-12T10:57:53,875 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:53,875 /usr/local/include 2023-09-12T10:57:53,876 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:53,876 /usr/include 2023-09-12T10:57:53,877 End of search list. 2023-09-12T10:57:53,878 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:53,878 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:57:53,880 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:53,880 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:53,881 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:57:55,444 In file included from include/openbabel/atom.h:33, 2023-09-12T10:57:55,445 from include/openbabel/mol.h:43, 2023-09-12T10:57:55,446 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:57:55,446 from ./src/formats/cacheformat.cpp:16: 2023-09-12T10:57:55,447 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:57:55,447 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:57:55,448 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:57:55,448 | ^ 2023-09-12T10:57:55,449 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:57:55,449 37 | # define UNUSED(x) x 2023-09-12T10:57:55,450 | ^ 2023-09-12T10:57:56,211 In file included from include/openbabel/mol.h:52: 2023-09-12T10:57:56,212 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:56,212 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:56,213 862 | {return new OBVibrationData(*this);} 2023-09-12T10:57:56,213 | ^ 2023-09-12T10:57:56,214 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:57:56,215 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:57:56,215 | ^~~~~~~~ 2023-09-12T10:57:56,216 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:56,217 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:56,218 907 | {return new OBDOSData(*this);} 2023-09-12T10:57:56,218 | ^ 2023-09-12T10:57:56,219 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:57:56,220 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:57:56,221 | ^~~~~~~~ 2023-09-12T10:57:56,235 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:56,236 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:56,237 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:57:56,237 | ^ 2023-09-12T10:57:56,238 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:57:56,239 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:57:56,239 | ^~~~~~~~ 2023-09-12T10:57:56,242 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:57:56,242 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:57:56,243 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:57:56,244 | ^ 2023-09-12T10:57:56,245 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:57:56,245 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:57:56,246 | ^~~~~~~~ 2023-09-12T10:57:56,415 In file included from include/openbabel/format.h:22, 2023-09-12T10:57:56,415 from include/openbabel/obconversion.h:37, 2023-09-12T10:57:56,416 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:57:56,416 include/openbabel/plugin.h: At global scope: 2023-09-12T10:57:56,417 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:57:56,417 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:57:56,418 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:56,418 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:57:56,419 from /usr/include/c++/12/vector:66, 2023-09-12T10:57:56,420 from include/openbabel/mol.h:35: 2023-09-12T10:57:56,420 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:57:56,421 131 | struct binary_function 2023-09-12T10:57:56,421 | ^~~~~~~~~~~~~~~ 2023-09-12T10:57:58,888 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/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/' 2023-09-12T10:57:58,889 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/ccOfref3.s 2023-09-12T10:57:58,893 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:57:59,035 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/ 2023-09-12T10:57:59,036 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/ 2023-09-12T10:57:59,036 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:57:59,037 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 2023-09-12T10:57:59,041 Using built-in specs. 2023-09-12T10:57:59,042 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:57:59,043 Target: arm-linux-gnueabihf 2023-09-12T10:57:59,043 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 2023-09-12T10:57:59,044 Thread model: posix 2023-09-12T10:57:59,044 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:57:59,045 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:57:59,045 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:57:59,046 /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/ccY0kFzh.s 2023-09-12T10:57:59,054 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:59,055 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 2023-09-12T10:57:59,056 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:59,056 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:59,057 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:57:59,057 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:57:59,058 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:57:59,059 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:57:59,059 ignoring duplicate directory "/usr/include/" 2023-09-12T10:57:59,060 as it is a non-system directory that duplicates a system directory 2023-09-12T10:57:59,061 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:57:59,061 #include "..." search starts here: 2023-09-12T10:57:59,062 #include <...> search starts here: 2023-09-12T10:57:59,063 /usr/include/eigen3 2023-09-12T10:57:59,063 include 2023-09-12T10:57:59,063 /usr/include/python3.11 2023-09-12T10:57:59,064 /usr/include/c++/12 2023-09-12T10:57:59,064 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:57:59,065 /usr/include/c++/12/backward 2023-09-12T10:57:59,065 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:57:59,066 /usr/local/include 2023-09-12T10:57:59,066 /usr/include/arm-linux-gnueabihf 2023-09-12T10:57:59,066 /usr/include 2023-09-12T10:57:59,067 End of search list. 2023-09-12T10:57:59,067 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:57:59,068 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 2023-09-12T10:57:59,069 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:57:59,069 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:57:59,072 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:00,630 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:00,631 from include/openbabel/mol.h:43, 2023-09-12T10:58:00,631 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:00,632 from ./src/formats/carformat.cpp:18: 2023-09-12T10:58:00,632 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:00,633 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:00,634 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:00,634 | ^ 2023-09-12T10:58:00,635 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:00,636 37 | # define UNUSED(x) x 2023-09-12T10:58:00,636 | ^ 2023-09-12T10:58:01,397 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:01,398 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:01,398 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:01,399 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:01,400 | ^ 2023-09-12T10:58:01,401 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:01,401 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:01,402 | ^~~~~~~~ 2023-09-12T10:58:01,403 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:01,403 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:01,404 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:01,405 | ^ 2023-09-12T10:58:01,405 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:01,406 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:01,407 | ^~~~~~~~ 2023-09-12T10:58:01,421 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:01,422 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:01,422 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:01,423 | ^ 2023-09-12T10:58:01,424 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:01,424 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:01,425 | ^~~~~~~~ 2023-09-12T10:58:01,427 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:01,428 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:01,429 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:01,429 | ^ 2023-09-12T10:58:01,430 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:01,430 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:01,431 | ^~~~~~~~ 2023-09-12T10:58:01,600 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:01,600 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:01,601 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:01,602 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:01,603 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:01,603 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:01,604 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:01,605 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:01,606 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:01,606 from include/openbabel/mol.h:35: 2023-09-12T10:58:01,607 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:01,608 131 | struct binary_function 2023-09-12T10:58:01,608 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:04,521 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:04,522 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/ccY0kFzh.s 2023-09-12T10:58:04,526 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:04,721 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/ 2023-09-12T10:58:04,722 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/ 2023-09-12T10:58:04,722 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:58:04,724 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/castepformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/castepformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:58:04,727 Using built-in specs. 2023-09-12T10:58:04,728 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:04,728 Target: arm-linux-gnueabihf 2023-09-12T10:58:04,729 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 2023-09-12T10:58:04,730 Thread model: posix 2023-09-12T10:58:04,730 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:04,731 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:04,732 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:04,732 /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/ccxkyvul.s 2023-09-12T10:58:04,742 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:04,743 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 2023-09-12T10:58:04,744 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:04,744 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:04,745 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:04,745 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:04,745 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:04,746 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:04,746 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:04,747 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:04,747 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:04,747 #include "..." search starts here: 2023-09-12T10:58:04,748 #include <...> search starts here: 2023-09-12T10:58:04,748 /usr/include/eigen3 2023-09-12T10:58:04,748 include 2023-09-12T10:58:04,749 /usr/include/python3.11 2023-09-12T10:58:04,749 /usr/include/c++/12 2023-09-12T10:58:04,750 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:04,750 /usr/include/c++/12/backward 2023-09-12T10:58:04,751 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:04,751 /usr/local/include 2023-09-12T10:58:04,752 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:04,752 /usr/include 2023-09-12T10:58:04,753 End of search list. 2023-09-12T10:58:04,754 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:04,754 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:04,755 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:04,756 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:04,767 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:06,324 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:06,325 from include/openbabel/mol.h:43, 2023-09-12T10:58:06,326 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:06,327 from ./src/formats/castepformat.cpp:16: 2023-09-12T10:58:06,327 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:06,328 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:06,328 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:06,329 | ^ 2023-09-12T10:58:06,330 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:06,330 37 | # define UNUSED(x) x 2023-09-12T10:58:06,331 | ^ 2023-09-12T10:58:07,094 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:07,095 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:07,096 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:07,096 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:07,097 | ^ 2023-09-12T10:58:07,098 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:07,099 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:07,099 | ^~~~~~~~ 2023-09-12T10:58:07,102 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:07,103 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:07,104 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:07,104 | ^ 2023-09-12T10:58:07,105 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:07,105 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:07,105 | ^~~~~~~~ 2023-09-12T10:58:07,123 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:07,124 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:07,125 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:07,125 | ^ 2023-09-12T10:58:07,126 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:07,127 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:07,127 | ^~~~~~~~ 2023-09-12T10:58:07,132 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:07,133 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:07,134 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:07,134 | ^ 2023-09-12T10:58:07,135 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:07,136 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:07,136 | ^~~~~~~~ 2023-09-12T10:58:07,307 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:07,307 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:07,308 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:07,309 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:07,309 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:07,310 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:07,311 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:07,311 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:07,312 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:07,313 from include/openbabel/mol.h:35: 2023-09-12T10:58:07,314 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:07,314 131 | struct binary_function 2023-09-12T10:58:07,314 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:07,509 ./src/formats/castepformat.cpp: In member function ‘virtual int OpenBabel::CASTEPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T10:58:07,510 ./src/formats/castepformat.cpp:50:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T10:58:07,510 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T10:58:07,511 | ~~~~^ 2023-09-12T10:58:07,511 ./src/formats/castepformat.cpp:50:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T10:58:07,512 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T10:58:07,512 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T10:58:09,981 ./src/formats/castepformat.cpp: In member function ‘virtual bool OpenBabel::CASTEPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:58:09,982 ./src/formats/castepformat.cpp:203:17: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:09,983 203 | snprintf(tag, BUFF_SIZE, "%f", enthalpy); 2023-09-12T10:58:09,983 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:09,984 ./src/formats/castepformat.cpp:86:30: note: ‘enthalpy’ was declared here 2023-09-12T10:58:09,985 86 | double pressure, volume, enthalpy; 2023-09-12T10:58:09,985 | ^~~~~~~~ 2023-09-12T10:58:09,986 ./src/formats/castepformat.cpp:187:21: warning: ‘volume’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:09,987 187 | pv = volume * pressure * GPA_A3_TO_KCAL_PER_MOL; 2023-09-12T10:58:09,988 | ~~~~~~~^~~~~~~~~~ 2023-09-12T10:58:09,988 ./src/formats/castepformat.cpp:86:22: note: ‘volume’ was declared here 2023-09-12T10:58:09,989 86 | double pressure, volume, enthalpy; 2023-09-12T10:58:09,990 | ^~~~~~ 2023-09-12T10:58:09,991 ./src/formats/castepformat.cpp:187:21: warning: ‘pressure’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:09,991 187 | pv = volume * pressure * GPA_A3_TO_KCAL_PER_MOL; 2023-09-12T10:58:09,992 | ~~~~~~~^~~~~~~~~~ 2023-09-12T10:58:09,993 ./src/formats/castepformat.cpp:86:12: note: ‘pressure’ was declared here 2023-09-12T10:58:09,993 86 | double pressure, volume, enthalpy; 2023-09-12T10:58:09,994 | ^~~~~~~~ 2023-09-12T10:58:10,603 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:10,604 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/ccxkyvul.s 2023-09-12T10:58:10,609 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:10,829 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/ 2023-09-12T10:58:10,830 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/ 2023-09-12T10:58:10,831 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:58:10,831 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 2023-09-12T10:58:10,835 Using built-in specs. 2023-09-12T10:58:10,836 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:10,836 Target: arm-linux-gnueabihf 2023-09-12T10:58:10,837 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 2023-09-12T10:58:10,837 Thread model: posix 2023-09-12T10:58:10,838 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:10,839 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:10,839 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:10,840 /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/ccqwqW8k.s 2023-09-12T10:58:10,848 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:10,849 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:10,850 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:10,851 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:10,851 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:10,852 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:10,852 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:10,853 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:10,853 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:10,854 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:10,854 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:10,854 #include "..." search starts here: 2023-09-12T10:58:10,855 #include <...> search starts here: 2023-09-12T10:58:10,855 /usr/include/eigen3 2023-09-12T10:58:10,856 include 2023-09-12T10:58:10,856 /usr/include/python3.11 2023-09-12T10:58:10,857 /usr/include/c++/12 2023-09-12T10:58:10,857 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:10,858 /usr/include/c++/12/backward 2023-09-12T10:58:10,858 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:10,859 /usr/local/include 2023-09-12T10:58:10,859 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:10,860 /usr/include 2023-09-12T10:58:10,860 End of search list. 2023-09-12T10:58:10,861 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:10,861 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:10,862 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:10,863 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:10,866 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:12,427 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:12,428 from include/openbabel/mol.h:43, 2023-09-12T10:58:12,428 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:12,429 from ./src/formats/cccformat.cpp:17: 2023-09-12T10:58:12,430 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:12,431 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:12,432 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:12,432 | ^ 2023-09-12T10:58:12,433 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:12,434 37 | # define UNUSED(x) x 2023-09-12T10:58:12,434 | ^ 2023-09-12T10:58:13,196 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:13,197 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:13,198 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:13,199 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:13,199 | ^ 2023-09-12T10:58:13,200 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:13,201 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:13,202 | ^~~~~~~~ 2023-09-12T10:58:13,203 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:13,203 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:13,204 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:13,204 | ^ 2023-09-12T10:58:13,205 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:13,205 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:13,206 | ^~~~~~~~ 2023-09-12T10:58:13,221 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:13,221 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:13,222 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:13,222 | ^ 2023-09-12T10:58:13,223 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:13,224 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:13,224 | ^~~~~~~~ 2023-09-12T10:58:13,227 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:13,228 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:13,228 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:13,229 | ^ 2023-09-12T10:58:13,230 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:13,231 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:13,232 | ^~~~~~~~ 2023-09-12T10:58:13,400 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:13,400 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:13,401 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:13,402 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:13,402 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:13,403 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:13,404 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:13,404 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:13,405 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:13,406 from include/openbabel/mol.h:35: 2023-09-12T10:58:13,407 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:13,407 131 | struct binary_function 2023-09-12T10:58:13,408 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:15,984 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:15,984 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/ccqwqW8k.s 2023-09-12T10:58:15,989 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:16,138 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/ 2023-09-12T10:58:16,139 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/ 2023-09-12T10:58:16,139 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/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.' 2023-09-12T10:58:16,141 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 2023-09-12T10:58:16,145 Using built-in specs. 2023-09-12T10:58:16,146 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:16,146 Target: arm-linux-gnueabihf 2023-09-12T10:58:16,147 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 2023-09-12T10:58:16,147 Thread model: posix 2023-09-12T10:58:16,148 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:16,149 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:16,149 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/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/' 2023-09-12T10:58:16,150 /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/ccDih6UP.s 2023-09-12T10:58:16,158 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:16,159 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 2023-09-12T10:58:16,160 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:16,160 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:16,161 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:16,161 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:16,162 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:16,163 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:16,163 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:16,164 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:16,164 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:16,165 #include "..." search starts here: 2023-09-12T10:58:16,166 #include <...> search starts here: 2023-09-12T10:58:16,166 /usr/include/eigen3 2023-09-12T10:58:16,167 include 2023-09-12T10:58:16,168 /usr/include/python3.11 2023-09-12T10:58:16,168 /usr/include/c++/12 2023-09-12T10:58:16,169 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:16,170 /usr/include/c++/12/backward 2023-09-12T10:58:16,170 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:16,171 /usr/local/include 2023-09-12T10:58:16,172 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:16,172 /usr/include 2023-09-12T10:58:16,173 End of search list. 2023-09-12T10:58:16,173 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:16,174 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 2023-09-12T10:58:16,175 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:16,175 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:16,176 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:17,829 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:17,830 from include/openbabel/mol.h:43, 2023-09-12T10:58:17,830 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:17,831 from ./src/formats/chem3dformat.cpp:18: 2023-09-12T10:58:17,832 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:17,833 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:17,833 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:17,834 | ^ 2023-09-12T10:58:17,835 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:17,835 37 | # define UNUSED(x) x 2023-09-12T10:58:17,836 | ^ 2023-09-12T10:58:18,497 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:18,498 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:18,498 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:18,499 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:18,500 | ^ 2023-09-12T10:58:18,500 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:18,501 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:18,501 | ^~~~~~~~ 2023-09-12T10:58:18,502 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:18,503 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:18,504 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:18,505 | ^ 2023-09-12T10:58:18,505 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:18,506 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:18,507 | ^~~~~~~~ 2023-09-12T10:58:18,521 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:18,522 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:18,523 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:18,524 | ^ 2023-09-12T10:58:18,524 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:18,525 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:18,526 | ^~~~~~~~ 2023-09-12T10:58:18,528 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:18,528 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:18,529 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:18,530 | ^ 2023-09-12T10:58:18,530 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:18,531 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:18,532 | ^~~~~~~~ 2023-09-12T10:58:18,700 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:18,701 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:18,702 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:18,702 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:18,703 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:18,703 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:18,704 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:18,704 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:58:18,705 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:58:18,706 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:58:18,706 from /usr/include/c++/12/ios:42, 2023-09-12T10:58:18,707 from /usr/include/c++/12/ostream:38, 2023-09-12T10:58:18,707 from include/openbabel/math/matrix3x3.h:24, 2023-09-12T10:58:18,708 from ./src/formats/chem3dformat.cpp:17: 2023-09-12T10:58:18,708 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:18,709 131 | struct binary_function 2023-09-12T10:58:18,709 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:21,075 ./src/formats/chem3dformat.cpp: In static member function ‘static bool OpenBabel::CHEM3D1Format::WriteChem3d(std::ostream&, OpenBabel::OBMol&, const char*)’: 2023-09-12T10:58:21,075 ./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=] 2023-09-12T10:58:21,076 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2023-09-12T10:58:21,077 | ^~ 2023-09-12T10:58:21,077 ./src/formats/chem3dformat.cpp:298:51: note: directive argument in the range [-536870912, 536873461] 2023-09-12T10:58:21,078 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2023-09-12T10:58:21,079 | ^~~~ 2023-09-12T10:58:21,080 ./src/formats/chem3dformat.cpp:298:21: note: ‘snprintf’ output between 2 and 11 bytes into a destination of size 4 2023-09-12T10:58:21,081 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2023-09-12T10:58:21,081 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:21,654 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:21,655 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/ccDih6UP.s 2023-09-12T10:58:21,659 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:21,841 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/ 2023-09-12T10:58:21,842 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/ 2023-09-12T10:58:21,843 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:58:21,844 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 2023-09-12T10:58:21,848 Using built-in specs. 2023-09-12T10:58:21,849 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:21,849 Target: arm-linux-gnueabihf 2023-09-12T10:58:21,850 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 2023-09-12T10:58:21,850 Thread model: posix 2023-09-12T10:58:21,851 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:21,852 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:21,852 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:21,853 /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/ccm3DiTL.s 2023-09-12T10:58:21,861 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:21,862 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:21,863 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:21,864 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:21,864 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:21,865 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:21,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:21,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:21,866 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:21,866 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:21,867 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:21,867 #include "..." search starts here: 2023-09-12T10:58:21,868 #include <...> search starts here: 2023-09-12T10:58:21,868 /usr/include/eigen3 2023-09-12T10:58:21,868 include 2023-09-12T10:58:21,869 /usr/include/python3.11 2023-09-12T10:58:21,869 /usr/include/c++/12 2023-09-12T10:58:21,870 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:21,870 /usr/include/c++/12/backward 2023-09-12T10:58:21,871 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:21,871 /usr/local/include 2023-09-12T10:58:21,872 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:21,872 /usr/include 2023-09-12T10:58:21,873 End of search list. 2023-09-12T10:58:21,873 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:21,874 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:21,875 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:21,875 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:21,879 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:23,460 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:23,461 from include/openbabel/mol.h:43, 2023-09-12T10:58:23,461 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:23,462 from ./src/formats/chemdrawcdx.cpp:17: 2023-09-12T10:58:23,463 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:23,464 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:23,464 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:23,465 | ^ 2023-09-12T10:58:23,466 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:23,466 37 | # define UNUSED(x) x 2023-09-12T10:58:23,467 | ^ 2023-09-12T10:58:24,227 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:24,228 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:24,228 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:24,229 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:24,230 | ^ 2023-09-12T10:58:24,230 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:24,231 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:24,232 | ^~~~~~~~ 2023-09-12T10:58:24,233 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:24,233 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:24,234 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:24,234 | ^ 2023-09-12T10:58:24,235 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:24,236 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:24,236 | ^~~~~~~~ 2023-09-12T10:58:24,252 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:24,253 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:24,254 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:24,254 | ^ 2023-09-12T10:58:24,255 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:24,256 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:24,256 | ^~~~~~~~ 2023-09-12T10:58:24,260 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:24,261 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:24,261 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:24,262 | ^ 2023-09-12T10:58:24,263 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:24,264 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:24,265 | ^~~~~~~~ 2023-09-12T10:58:24,433 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:24,434 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:24,435 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:24,436 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:24,436 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:24,437 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:24,438 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:24,438 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:24,439 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:24,440 from include/openbabel/mol.h:35: 2023-09-12T10:58:24,441 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:24,441 131 | struct binary_function 2023-09-12T10:58:24,442 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:25,092 ./src/formats/chemdrawcdx.cpp: In member function ‘virtual bool OpenBabel::ChemDrawBinaryXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:58:25,092 ./src/formats/chemdrawcdx.cpp:205:50: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2023-09-12T10:58:25,093 205 | bool ChemDrawBinaryXFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) 2023-09-12T10:58:25,094 | ~~~~~~~~^~~ 2023-09-12T10:58:25,140 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoReaction(OpenBabel::CDXReader&, OpenBabel::OBReaction*)’: 2023-09-12T10:58:25,140 ./src/formats/chemdrawcdx.cpp:331:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T10:58:25,141 331 | for(unsigned i=0;iNumAtoms();++idx) 2023-09-12T10:58:25,234 | ~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T10:58:25,239 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2023-09-12T10:58:25,240 ./src/formats/chemdrawcdx.cpp:454:27: warning: variable ‘hasElement’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:58:25,241 454 | bool isAlias=false, hasElement=false; 2023-09-12T10:58:25,241 | ^~~~~~~~~~ 2023-09-12T10:58:25,245 ./src/formats/chemdrawcdx.cpp:446:84: warning: unused parameter ‘updown’ [-Wunused-parameter] 2023-09-12T10:58:25,246 446 | map& atommap, map& updown) 2023-09-12T10:58:25,247 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-09-12T10:58:27,251 ./src/formats/chemdrawcdx.cpp: In member function ‘std::string OpenBabel::ChemDrawBinaryXFormat::DoText(OpenBabel::CDXReader&)’: 2023-09-12T10:58:27,252 ./src/formats/chemdrawcdx.cpp:625:13: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T10:58:27,253 625 | ss >> text; 2023-09-12T10:58:27,253 | ^~~~ 2023-09-12T10:58:27,254 ./src/formats/chemdrawcdx.cpp:626:5: note: here 2023-09-12T10:58:27,255 626 | default: 2023-09-12T10:58:27,255 | ^~~~~~~ 2023-09-12T10:58:33,777 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2023-09-12T10:58:33,777 ./src/formats/chemdrawcdx.cpp:591:28: warning: ‘endIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:33,778 591 | if(!order || !bgnIdx || !endIdx) 2023-09-12T10:58:33,779 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:58:33,780 ./src/formats/chemdrawcdx.cpp:550:28: note: ‘endIdx’ was declared here 2023-09-12T10:58:33,781 550 | int order=1, bgnIdx, endIdx ; 2023-09-12T10:58:33,781 | ^~~~~~ 2023-09-12T10:58:33,782 ./src/formats/chemdrawcdx.cpp:591:17: warning: ‘bgnIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:58:33,782 591 | if(!order || !bgnIdx || !endIdx) 2023-09-12T10:58:33,783 | ~~~~~~~^~~~~~~~~~ 2023-09-12T10:58:33,783 ./src/formats/chemdrawcdx.cpp:550:20: note: ‘bgnIdx’ was declared here 2023-09-12T10:58:33,784 550 | int order=1, bgnIdx, endIdx ; 2023-09-12T10:58:33,785 | ^~~~~~ 2023-09-12T10:58:35,947 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:58:35,948 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/ccm3DiTL.s 2023-09-12T10:58:35,960 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:36,766 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/ 2023-09-12T10:58:36,766 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/ 2023-09-12T10:58:36,767 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:58:36,771 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 2023-09-12T10:58:36,776 Using built-in specs. 2023-09-12T10:58:36,777 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:36,778 Target: arm-linux-gnueabihf 2023-09-12T10:58:36,778 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 2023-09-12T10:58:36,779 Thread model: posix 2023-09-12T10:58:36,780 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:36,780 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:36,781 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/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/' 2023-09-12T10:58:36,781 /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/ccGS80yj.s 2023-09-12T10:58:36,791 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:36,792 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:36,793 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:36,793 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:36,794 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:36,794 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:36,795 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:36,796 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:36,796 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:36,797 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:36,798 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:36,798 #include "..." search starts here: 2023-09-12T10:58:36,799 #include <...> search starts here: 2023-09-12T10:58:36,800 /usr/include/eigen3 2023-09-12T10:58:36,800 include 2023-09-12T10:58:36,801 /usr/include/python3.11 2023-09-12T10:58:36,801 /usr/include/c++/12 2023-09-12T10:58:36,802 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:36,802 /usr/include/c++/12/backward 2023-09-12T10:58:36,803 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:36,803 /usr/local/include 2023-09-12T10:58:36,804 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:36,805 /usr/include 2023-09-12T10:58:36,805 End of search list. 2023-09-12T10:58:36,806 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:36,807 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:36,808 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:36,809 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:36,811 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:38,369 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:38,370 from include/openbabel/mol.h:43, 2023-09-12T10:58:38,371 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:58:38,371 from ./src/formats/chemdrawct.cpp:16: 2023-09-12T10:58:38,372 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:38,372 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:38,373 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:38,373 | ^ 2023-09-12T10:58:38,374 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:38,374 37 | # define UNUSED(x) x 2023-09-12T10:58:38,375 | ^ 2023-09-12T10:58:39,136 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:39,137 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:39,138 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:39,138 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:39,139 | ^ 2023-09-12T10:58:39,140 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:39,140 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:39,141 | ^~~~~~~~ 2023-09-12T10:58:39,142 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:39,143 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:39,143 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:39,144 | ^ 2023-09-12T10:58:39,145 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:39,146 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:39,146 | ^~~~~~~~ 2023-09-12T10:58:39,161 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:39,161 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:39,162 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:39,163 | ^ 2023-09-12T10:58:39,164 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:39,164 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:39,165 | ^~~~~~~~ 2023-09-12T10:58:39,167 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:39,168 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:39,169 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:39,170 | ^ 2023-09-12T10:58:39,171 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:39,171 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:39,172 | ^~~~~~~~ 2023-09-12T10:58:39,340 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:39,340 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:39,341 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:58:39,342 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:39,342 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:39,343 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:39,343 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:39,344 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:58:39,344 from /usr/include/c++/12/vector:66, 2023-09-12T10:58:39,345 from include/openbabel/mol.h:35: 2023-09-12T10:58:39,346 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:39,346 131 | struct binary_function 2023-09-12T10:58:39,347 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:39,551 ./src/formats/chemdrawct.cpp: In member function ‘virtual bool OpenBabel::ChemDrawFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T10:58:39,552 ./src/formats/chemdrawct.cpp:130:22: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:58:39,552 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2023-09-12T10:58:39,553 | ~^ ~~~~~~~ 2023-09-12T10:58:39,554 | | | 2023-09-12T10:58:39,555 | int* unsigned int* 2023-09-12T10:58:39,556 | %d 2023-09-12T10:58:39,556 ./src/formats/chemdrawct.cpp:130:25: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:58:39,557 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2023-09-12T10:58:39,558 | ~^ ~~~~~~~ 2023-09-12T10:58:39,559 | | | 2023-09-12T10:58:39,559 | int* unsigned int* 2023-09-12T10:58:39,560 | %d 2023-09-12T10:58:39,561 ./src/formats/chemdrawct.cpp:153:32: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:58:39,561 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2023-09-12T10:58:39,562 | ~^ ~~~~ 2023-09-12T10:58:39,563 | | | 2023-09-12T10:58:39,564 | int* unsigned int* 2023-09-12T10:58:39,564 | %d 2023-09-12T10:58:39,565 ./src/formats/chemdrawct.cpp:153:34: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:58:39,566 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2023-09-12T10:58:39,567 | ~^ ~~~~ 2023-09-12T10:58:39,568 | | | 2023-09-12T10:58:39,568 | int* unsigned int* 2023-09-12T10:58:39,569 | %d 2023-09-12T10:58:39,570 ./src/formats/chemdrawct.cpp:153:36: warning: format ‘%d’ expects argument of type ‘int*’, but argument 5 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T10:58:39,570 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2023-09-12T10:58:39,571 | ~^ ~~~~~~ 2023-09-12T10:58:39,571 | | | 2023-09-12T10:58:39,572 | int* unsigned int* 2023-09-12T10:58:39,572 | %d 2023-09-12T10:58:42,679 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/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/' 2023-09-12T10:58:42,680 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/chemdrawct.o /tmp/ccGS80yj.s 2023-09-12T10:58:42,692 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:58:42,885 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/ 2023-09-12T10:58:42,885 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/ 2023-09-12T10:58:42,886 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:58:42,888 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 2023-09-12T10:58:42,892 Using built-in specs. 2023-09-12T10:58:42,893 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:58:42,893 Target: arm-linux-gnueabihf 2023-09-12T10:58:42,894 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 2023-09-12T10:58:42,895 Thread model: posix 2023-09-12T10:58:42,895 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:58:42,896 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:58:42,896 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/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/' 2023-09-12T10:58:42,897 /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/ccqv0wNB.s 2023-09-12T10:58:42,905 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:42,906 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:58:42,907 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:42,907 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:42,908 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:58:42,909 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:58:42,909 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:58:42,910 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:58:42,911 ignoring duplicate directory "/usr/include/" 2023-09-12T10:58:42,911 as it is a non-system directory that duplicates a system directory 2023-09-12T10:58:42,912 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:58:42,912 #include "..." search starts here: 2023-09-12T10:58:42,913 #include <...> search starts here: 2023-09-12T10:58:42,913 /usr/include/eigen3 2023-09-12T10:58:42,914 include 2023-09-12T10:58:42,915 /usr/include/python3.11 2023-09-12T10:58:42,915 /usr/include/c++/12 2023-09-12T10:58:42,916 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:58:42,916 /usr/include/c++/12/backward 2023-09-12T10:58:42,917 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:58:42,918 /usr/local/include 2023-09-12T10:58:42,918 /usr/include/arm-linux-gnueabihf 2023-09-12T10:58:42,919 /usr/include 2023-09-12T10:58:42,920 End of search list. 2023-09-12T10:58:42,920 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:58:42,921 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 2023-09-12T10:58:42,923 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:58:42,924 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:58:42,924 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:58:44,657 In file included from include/openbabel/atom.h:33, 2023-09-12T10:58:44,657 from include/openbabel/mol.h:43, 2023-09-12T10:58:44,658 from ./src/formats/chemkinformat.cpp:25: 2023-09-12T10:58:44,659 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:58:44,659 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:58:44,660 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:58:44,660 | ^ 2023-09-12T10:58:44,661 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:58:44,661 37 | # define UNUSED(x) x 2023-09-12T10:58:44,662 | ^ 2023-09-12T10:58:45,423 In file included from include/openbabel/mol.h:52: 2023-09-12T10:58:45,424 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:45,424 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:45,425 862 | {return new OBVibrationData(*this);} 2023-09-12T10:58:45,426 | ^ 2023-09-12T10:58:45,426 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:58:45,427 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:58:45,428 | ^~~~~~~~ 2023-09-12T10:58:45,429 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:45,430 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:45,431 907 | {return new OBDOSData(*this);} 2023-09-12T10:58:45,432 | ^ 2023-09-12T10:58:45,433 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:58:45,433 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:58:45,434 | ^~~~~~~~ 2023-09-12T10:58:45,448 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:45,449 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:45,450 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:58:45,450 | ^ 2023-09-12T10:58:45,451 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:58:45,452 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:58:45,453 | ^~~~~~~~ 2023-09-12T10:58:45,456 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:45,457 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:58:45,457 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:58:45,458 | ^ 2023-09-12T10:58:45,459 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:58:45,459 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:58:45,460 | ^~~~~~~~ 2023-09-12T10:58:45,629 In file included from include/openbabel/format.h:22, 2023-09-12T10:58:45,629 from include/openbabel/obconversion.h:37, 2023-09-12T10:58:45,630 from ./src/formats/chemkinformat.cpp:27: 2023-09-12T10:58:45,631 include/openbabel/plugin.h: At global scope: 2023-09-12T10:58:45,631 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:58:45,632 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:58:45,632 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:45,633 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:58:45,634 from ./src/formats/chemkinformat.cpp:18: 2023-09-12T10:58:45,635 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:58:45,635 131 | struct binary_function 2023-09-12T10:58:45,636 | ^~~~~~~~~~~~~~~ 2023-09-12T10:58:45,986 In file included from ./src/formats/chemkinformat.cpp:29: 2023-09-12T10:58:45,987 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:45,987 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T10:58:45,988 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2023-09-12T10:58:45,989 | ~~~~~~~~^~~~~~ 2023-09-12T10:58:46,008 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:58:46,009 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T10:58:46,010 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2023-09-12T10:58:46,010 | ~~~~~~~~^~~~~~ 2023-09-12T10:58:46,172 ./src/formats/chemkinformat.cpp: In member function ‘bool OpenBabel::ChemKinFormat::ReadReactionQualifierLines(std::istream&, OpenBabel::OBReaction*)’: 2023-09-12T10:58:46,172 ./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] 2023-09-12T10:58:46,173 634 | for(int i=0;iReactionType) 2023-09-12T10:58:46,284 | ^ 2023-09-12T10:58:46,285 ./src/formats/chemkinformat.cpp:905:11: warning: enumeration value ‘THREEBODY’ not handled in switch [-Wswitch] 2023-09-12T10:58:46,319 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘ARRHENIUS’ not handled in switch [-Wswitch] 2023-09-12T10:58:46,320 984 | switch(pRD->ReactionType) 2023-09-12T10:58:46,320 | ^ 2023-09-12T10:58:46,321 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘SRI’ not handled in switch [-Wswitch] 2023-09-12T10:59:00,642 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/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/' 2023-09-12T10:59:00,642 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/ccqv0wNB.s 2023-09-12T10:59:00,647 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:01,876 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/ 2023-09-12T10:59:01,877 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/ 2023-09-12T10:59:01,878 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:59:01,882 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 2023-09-12T10:59:01,886 Using built-in specs. 2023-09-12T10:59:01,887 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:01,887 Target: arm-linux-gnueabihf 2023-09-12T10:59:01,888 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 2023-09-12T10:59:01,889 Thread model: posix 2023-09-12T10:59:01,889 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:01,890 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:01,890 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/' 2023-09-12T10:59:01,891 /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/ccTIrgq2.s 2023-09-12T10:59:01,899 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:01,900 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:01,901 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:01,901 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:01,902 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:01,903 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:01,904 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:01,905 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:01,905 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:01,906 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:01,907 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:01,907 #include "..." search starts here: 2023-09-12T10:59:01,908 #include <...> search starts here: 2023-09-12T10:59:01,908 /usr/include/eigen3 2023-09-12T10:59:01,909 include 2023-09-12T10:59:01,910 /usr/include/python3.11 2023-09-12T10:59:01,910 /usr/include/c++/12 2023-09-12T10:59:01,911 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:01,911 /usr/include/c++/12/backward 2023-09-12T10:59:01,912 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:01,913 /usr/local/include 2023-09-12T10:59:01,913 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:01,914 /usr/include 2023-09-12T10:59:01,914 End of search list. 2023-09-12T10:59:01,915 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:01,916 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:01,917 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:01,918 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:01,918 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:03,486 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:03,487 from include/openbabel/mol.h:43, 2023-09-12T10:59:03,488 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:03,488 from ./src/formats/chemtoolformat.cpp:19: 2023-09-12T10:59:03,489 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:03,489 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:03,490 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:03,490 | ^ 2023-09-12T10:59:03,491 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:03,491 37 | # define UNUSED(x) x 2023-09-12T10:59:03,492 | ^ 2023-09-12T10:59:04,257 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:04,258 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:04,259 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:04,259 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:04,260 | ^ 2023-09-12T10:59:04,260 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:04,261 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:04,262 | ^~~~~~~~ 2023-09-12T10:59:04,263 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:04,263 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:04,264 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:04,265 | ^ 2023-09-12T10:59:04,265 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:04,266 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:04,267 | ^~~~~~~~ 2023-09-12T10:59:04,282 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:04,282 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:04,283 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:04,284 | ^ 2023-09-12T10:59:04,284 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:04,285 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:04,286 | ^~~~~~~~ 2023-09-12T10:59:04,288 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:04,289 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:04,290 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:04,290 | ^ 2023-09-12T10:59:04,291 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:04,292 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:04,292 | ^~~~~~~~ 2023-09-12T10:59:04,461 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:04,462 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:04,462 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:04,463 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:04,464 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:04,464 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:04,465 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:04,465 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:04,466 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:04,466 from include/openbabel/mol.h:35: 2023-09-12T10:59:04,467 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:04,468 131 | struct binary_function 2023-09-12T10:59:04,469 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:07,004 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:59:07,005 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/ccTIrgq2.s 2023-09-12T10:59:07,009 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:07,164 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/ 2023-09-12T10:59:07,166 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/ 2023-09-12T10:59:07,167 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/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.' 2023-09-12T10:59:07,167 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 2023-09-12T10:59:07,170 Using built-in specs. 2023-09-12T10:59:07,171 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:07,171 Target: arm-linux-gnueabihf 2023-09-12T10:59:07,172 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 2023-09-12T10:59:07,172 Thread model: posix 2023-09-12T10:59:07,173 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:07,173 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:07,174 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/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/' 2023-09-12T10:59:07,174 /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/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/cc7b1GtC.s 2023-09-12T10:59:07,183 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:07,183 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 2023-09-12T10:59:07,184 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:07,185 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:07,185 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:07,186 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:07,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:07,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:07,188 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:07,189 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:07,190 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:07,190 #include "..." search starts here: 2023-09-12T10:59:07,190 #include <...> search starts here: 2023-09-12T10:59:07,191 /usr/include/eigen3 2023-09-12T10:59:07,191 include 2023-09-12T10:59:07,192 /usr/include/python3.11 2023-09-12T10:59:07,192 /usr/include/c++/12 2023-09-12T10:59:07,193 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:07,193 /usr/include/c++/12/backward 2023-09-12T10:59:07,193 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:07,194 /usr/local/include 2023-09-12T10:59:07,194 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:07,195 /usr/include 2023-09-12T10:59:07,195 End of search list. 2023-09-12T10:59:07,196 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:07,196 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 2023-09-12T10:59:07,197 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:07,197 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:07,201 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:08,765 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:08,766 from include/openbabel/mol.h:43, 2023-09-12T10:59:08,766 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:08,767 from ./src/formats/cifformat.cpp:20: 2023-09-12T10:59:08,767 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:08,768 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:08,769 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:08,769 | ^ 2023-09-12T10:59:08,770 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:08,771 37 | # define UNUSED(x) x 2023-09-12T10:59:08,772 | ^ 2023-09-12T10:59:09,533 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:09,533 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:09,534 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:09,535 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:09,536 | ^ 2023-09-12T10:59:09,536 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:09,537 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:09,538 | ^~~~~~~~ 2023-09-12T10:59:09,539 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:09,540 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:09,541 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:09,541 | ^ 2023-09-12T10:59:09,542 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:09,543 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:09,544 | ^~~~~~~~ 2023-09-12T10:59:09,560 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:09,560 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:09,561 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:09,561 | ^ 2023-09-12T10:59:09,562 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:09,562 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:09,563 | ^~~~~~~~ 2023-09-12T10:59:09,567 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:09,568 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:09,568 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:09,569 | ^ 2023-09-12T10:59:09,569 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:09,570 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:09,570 | ^~~~~~~~ 2023-09-12T10:59:09,741 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:09,741 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:09,742 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:09,743 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:09,743 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:09,744 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:09,745 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:09,746 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:09,746 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:09,747 from include/openbabel/mol.h:35: 2023-09-12T10:59:09,748 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:09,748 131 | struct binary_function 2023-09-12T10:59:09,749 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:10,340 ./src/formats/cifformat.cpp: In member function ‘void OpenBabel::CIFData::CalcMatrices()’: 2023-09-12T10:59:10,341 ./src/formats/cifformat.cpp:900:11: warning: variable ‘aa’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:59:10,342 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T10:59:10,342 | ^~ 2023-09-12T10:59:10,343 ./src/formats/cifformat.cpp:900:14: warning: variable ‘bb’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:59:10,344 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T10:59:10,345 | ^~ 2023-09-12T10:59:10,345 ./src/formats/cifformat.cpp:900:27: warning: variable ‘betaa’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:59:10,346 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T10:59:10,347 | ^~~~~ 2023-09-12T10:59:10,348 ./src/formats/cifformat.cpp:900:33: warning: variable ‘gammaa’ set but not used [-Wunused-but-set-variable] 2023-09-12T10:59:10,348 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2023-09-12T10:59:10,349 | ^~~~~~ 2023-09-12T10:59:22,238 In file included from /usr/include/c++/12/map:60, 2023-09-12T10:59:22,238 from include/openbabel/mol.h:37: 2023-09-12T10:59:22,239 /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> >]’: 2023-09-12T10:59:22,240 /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 2023-09-12T10:59:22,240 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T10:59:22,241 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:22,459 In file included from /usr/include/c++/12/map:61: 2023-09-12T10:59:22,459 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> >]’, 2023-09-12T10:59:22,460 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:876:39: 2023-09-12T10:59:22,461 /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 2023-09-12T10:59:22,462 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:59:22,462 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:22,463 512 | std::tuple(__k), 2023-09-12T10:59:22,464 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:22,464 513 | std::tuple<>()); 2023-09-12T10:59:22,465 | ~~~~~~~~~~~~~~~ 2023-09-12T10:59:22,466 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> >]’, 2023-09-12T10:59:22,466 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:887:37: 2023-09-12T10:59:22,467 /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 2023-09-12T10:59:22,468 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T10:59:22,468 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:22,469 512 | std::tuple(__k), 2023-09-12T10:59:22,469 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:22,470 513 | std::tuple<>()); 2023-09-12T10:59:22,470 | ~~~~~~~~~~~~~~~ 2023-09-12T10:59:28,946 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:59:28,947 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/cc7b1GtC.s 2023-09-12T10:59:28,951 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:30,499 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/ 2023-09-12T10:59:30,500 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/ 2023-09-12T10:59:30,500 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:59:30,507 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 2023-09-12T10:59:30,511 Using built-in specs. 2023-09-12T10:59:30,512 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:30,513 Target: arm-linux-gnueabihf 2023-09-12T10:59:30,513 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 2023-09-12T10:59:30,514 Thread model: posix 2023-09-12T10:59:30,515 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:30,516 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:30,516 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:59:30,517 /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/ccJ9wnHy.s 2023-09-12T10:59:30,525 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:30,526 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:30,527 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:30,527 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:30,528 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:30,528 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:30,529 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:30,530 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:30,530 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:30,531 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:30,532 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:30,532 #include "..." search starts here: 2023-09-12T10:59:30,533 #include <...> search starts here: 2023-09-12T10:59:30,533 /usr/include/eigen3 2023-09-12T10:59:30,534 include 2023-09-12T10:59:30,534 /usr/include/python3.11 2023-09-12T10:59:30,535 /usr/include/c++/12 2023-09-12T10:59:30,536 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:30,536 /usr/include/c++/12/backward 2023-09-12T10:59:30,537 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:30,538 /usr/local/include 2023-09-12T10:59:30,538 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:30,539 /usr/include 2023-09-12T10:59:30,540 End of search list. 2023-09-12T10:59:30,541 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:30,541 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:30,542 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:30,542 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:30,547 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:32,500 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:32,533 from include/openbabel/mol.h:43, 2023-09-12T10:59:32,540 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:32,576 from ./src/formats/confabreport.cpp:34: 2023-09-12T10:59:32,613 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:32,625 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:32,656 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:32,663 | ^ 2023-09-12T10:59:32,826 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:32,840 37 | # define UNUSED(x) x 2023-09-12T10:59:32,841 | ^ 2023-09-12T10:59:33,366 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:33,366 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,367 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,368 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:33,368 | ^ 2023-09-12T10:59:33,369 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:33,370 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:33,371 | ^~~~~~~~ 2023-09-12T10:59:33,372 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,373 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,374 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:33,374 | ^ 2023-09-12T10:59:33,375 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:33,376 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:33,377 | ^~~~~~~~ 2023-09-12T10:59:33,392 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,393 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,394 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:33,395 | ^ 2023-09-12T10:59:33,395 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:33,396 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:33,397 | ^~~~~~~~ 2023-09-12T10:59:33,400 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:33,401 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:33,401 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:33,402 | ^ 2023-09-12T10:59:33,402 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:33,403 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:33,403 | ^~~~~~~~ 2023-09-12T10:59:33,574 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:33,574 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:33,575 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:33,576 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:33,576 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:33,577 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:33,578 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:33,579 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:33,580 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:33,580 from include/openbabel/mol.h:35: 2023-09-12T10:59:33,581 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:33,582 131 | struct binary_function 2023-09-12T10:59:33,583 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:35,342 ./src/formats/confabreport.cpp: In member function ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’: 2023-09-12T10:59:35,343 ./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] 2023-09-12T10:59:35,344 128 | for (int i=1; i < binvals.size(); i++) 2023-09-12T10:59:35,345 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T10:59:35,345 ./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] 2023-09-12T10:59:35,346 133 | for (int i=1; i < cumbins.size(); i++) 2023-09-12T10:59:35,347 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T10:59:37,449 In file included from /usr/include/c++/12/bits/stl_algo.h:60, 2023-09-12T10:59:37,450 from /usr/include/c++/12/algorithm:61, 2023-09-12T10:59:37,450 from include/openbabel/ring.h:24, 2023-09-12T10:59:37,451 from include/openbabel/mol.h:51: 2023-09-12T10:59:37,452 /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]’: 2023-09-12T10:59:37,452 /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 2023-09-12T10:59:37,453 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-12T10:59:37,454 | ^~~~~~~~~~~~~ 2023-09-12T10:59:37,479 /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]’: 2023-09-12T10:59:37,480 /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 2023-09-12T10:59:37,481 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-12T10:59:37,481 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:59:37,482 /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 2023-09-12T10:59:37,532 /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]’: 2023-09-12T10:59:37,532 /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 2023-09-12T10:59:37,533 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-12T10:59:37,533 | ^~~~~~~~~~~~~~~~ 2023-09-12T10:59:37,534 /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 2023-09-12T10:59:37,535 /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 2023-09-12T10:59:37,536 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-12T10:59:37,536 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:38,199 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2023-09-12T10:59:38,200 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, 2023-09-12T10:59:38,200 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2023-09-12T10:59:38,201 /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 2023-09-12T10:59:38,202 1937 | std::__introsort_loop(__first, __last, 2023-09-12T10:59:38,203 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:59:38,203 1938 | std::__lg(__last - __first) * 2, 2023-09-12T10:59:38,204 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:38,205 1939 | __comp); 2023-09-12T10:59:38,205 | ~~~~~~~ 2023-09-12T10:59:38,206 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2023-09-12T10:59:38,207 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, 2023-09-12T10:59:38,208 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, 2023-09-12T10:59:38,209 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2023-09-12T10:59:38,209 /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 2023-09-12T10:59:38,210 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-12T10:59:38,210 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:38,210 /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 2023-09-12T10:59:38,211 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-12T10:59:38,211 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:38,339 In file included from /usr/include/c++/12/vector:70: 2023-09-12T10:59:38,339 /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]’: 2023-09-12T10:59:38,340 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:38,340 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:59:38,341 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:38,454 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:38,454 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, 2023-09-12T10:59:38,455 inlined from ‘virtual bool OpenBabel::ConfabReport::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/confabreport.cpp:212:17: 2023-09-12T10:59:38,456 /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 2023-09-12T10:59:38,456 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:38,457 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:39,143 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/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/' 2023-09-12T10:59:39,144 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/ccJ9wnHy.s 2023-09-12T10:59:39,152 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:39,460 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/ 2023-09-12T10:59:39,461 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/ 2023-09-12T10:59:39,462 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:59:39,463 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 2023-09-12T10:59:39,468 Using built-in specs. 2023-09-12T10:59:39,468 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:39,469 Target: arm-linux-gnueabihf 2023-09-12T10:59:39,470 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 2023-09-12T10:59:39,470 Thread model: posix 2023-09-12T10:59:39,471 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:39,471 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:39,472 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:59:39,472 /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/ccRKJFf4.s 2023-09-12T10:59:39,481 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:39,482 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:39,483 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:39,484 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:39,484 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:39,485 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:39,485 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:39,486 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:39,486 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:39,487 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:39,487 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:39,488 #include "..." search starts here: 2023-09-12T10:59:39,488 #include <...> search starts here: 2023-09-12T10:59:39,489 /usr/include/eigen3 2023-09-12T10:59:39,489 include 2023-09-12T10:59:39,490 /usr/include/python3.11 2023-09-12T10:59:39,490 /usr/include/c++/12 2023-09-12T10:59:39,490 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:39,491 /usr/include/c++/12/backward 2023-09-12T10:59:39,492 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:39,492 /usr/local/include 2023-09-12T10:59:39,493 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:39,493 /usr/include 2023-09-12T10:59:39,494 End of search list. 2023-09-12T10:59:39,494 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:39,495 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:39,496 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:39,497 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:39,503 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:40,952 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:40,952 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:40,953 from ./src/formats/copyformat.cpp:14: 2023-09-12T10:59:40,954 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:40,955 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:40,956 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:40,956 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:59:40,957 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:59:40,957 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:59:40,958 from /usr/include/c++/12/ios:42, 2023-09-12T10:59:40,959 from /usr/include/c++/12/ostream:38, 2023-09-12T10:59:40,959 from /usr/include/c++/12/iostream:39, 2023-09-12T10:59:40,960 from include/openbabel/obconversion.h:24: 2023-09-12T10:59:40,961 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:40,961 131 | struct binary_function 2023-09-12T10:59:40,962 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:41,828 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/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/' 2023-09-12T10:59:41,829 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/ccRKJFf4.s 2023-09-12T10:59:41,833 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:41,890 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/ 2023-09-12T10:59:41,891 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/ 2023-09-12T10:59:41,892 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:59:41,893 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/crkformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/crkformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T10:59:41,896 Using built-in specs. 2023-09-12T10:59:41,897 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:41,898 Target: arm-linux-gnueabihf 2023-09-12T10:59:41,898 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 2023-09-12T10:59:41,899 Thread model: posix 2023-09-12T10:59:41,900 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:41,900 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:41,901 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/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/' 2023-09-12T10:59:41,901 /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/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/ccqZIicb.s 2023-09-12T10:59:41,910 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:41,910 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 2023-09-12T10:59:41,911 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:41,912 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:41,912 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:41,912 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:41,913 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:41,913 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:41,914 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:41,914 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:41,915 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:41,915 #include "..." search starts here: 2023-09-12T10:59:41,916 #include <...> search starts here: 2023-09-12T10:59:41,917 /usr/include/eigen3 2023-09-12T10:59:41,917 include 2023-09-12T10:59:41,918 /usr/include/python3.11 2023-09-12T10:59:41,918 /usr/include/c++/12 2023-09-12T10:59:41,919 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:41,919 /usr/include/c++/12/backward 2023-09-12T10:59:41,920 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:41,921 /usr/local/include 2023-09-12T10:59:41,921 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:41,922 /usr/include 2023-09-12T10:59:41,923 End of search list. 2023-09-12T10:59:41,923 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:41,924 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:41,925 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:41,926 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:41,927 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:43,492 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:43,493 from include/openbabel/mol.h:43, 2023-09-12T10:59:43,493 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:43,494 from ./src/formats/crkformat.cpp:16: 2023-09-12T10:59:43,495 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:43,495 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:43,496 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:43,496 | ^ 2023-09-12T10:59:43,497 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:43,498 37 | # define UNUSED(x) x 2023-09-12T10:59:43,499 | ^ 2023-09-12T10:59:44,263 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:44,264 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,264 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,265 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:44,266 | ^ 2023-09-12T10:59:44,266 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:44,267 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:44,268 | ^~~~~~~~ 2023-09-12T10:59:44,268 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,269 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,269 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:44,270 | ^ 2023-09-12T10:59:44,271 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:44,271 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:44,272 | ^~~~~~~~ 2023-09-12T10:59:44,287 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,288 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,289 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:44,289 | ^ 2023-09-12T10:59:44,290 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:44,291 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:44,291 | ^~~~~~~~ 2023-09-12T10:59:44,294 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:44,294 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:44,295 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:44,296 | ^ 2023-09-12T10:59:44,296 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:44,297 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:44,298 | ^~~~~~~~ 2023-09-12T10:59:44,466 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:44,467 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:44,468 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:44,468 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:44,469 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:44,470 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:44,470 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:44,471 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T10:59:44,472 from /usr/include/c++/12/vector:66, 2023-09-12T10:59:44,472 from include/openbabel/mol.h:35: 2023-09-12T10:59:44,473 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:44,473 131 | struct binary_function 2023-09-12T10:59:44,474 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:47,515 ./src/formats/crkformat.cpp: In static member function ‘static bool OpenBabel::CRK2DFormat::ReadCRK(std::istream&, OpenBabel::OBMol&, const char*)’: 2023-09-12T10:59:47,516 ./src/formats/crkformat.cpp:304:38: warning: ‘bondStyle’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,517 304 | stbondStyle[numBonds]=bondStyle; 2023-09-12T10:59:47,517 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T10:59:47,517 ./src/formats/crkformat.cpp:243:25: note: ‘bondStyle’ was declared here 2023-09-12T10:59:47,518 243 | int bondFrom,bondTo,bondStyle; 2023-09-12T10:59:47,518 | ^~~~~~~~~ 2023-09-12T10:59:47,519 ./src/formats/crkformat.cpp:302:35: warning: ‘bondTo’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,520 302 | stbondTo[numBonds]=bondTo; 2023-09-12T10:59:47,520 | ~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T10:59:47,521 ./src/formats/crkformat.cpp:243:18: note: ‘bondTo’ was declared here 2023-09-12T10:59:47,522 243 | int bondFrom,bondTo,bondStyle; 2023-09-12T10:59:47,523 | ^~~~~~ 2023-09-12T10:59:47,523 ./src/formats/crkformat.cpp:301:37: warning: ‘bondFrom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,524 301 | stbondFrom[numBonds]=bondFrom; 2023-09-12T10:59:47,525 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T10:59:47,526 ./src/formats/crkformat.cpp:243:9: note: ‘bondFrom’ was declared here 2023-09-12T10:59:47,526 243 | int bondFrom,bondTo,bondStyle; 2023-09-12T10:59:47,527 | ^~~~~~~~ 2023-09-12T10:59:47,528 ./src/formats/crkformat.cpp:287:36: warning: ‘atomCharge’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,529 287 | atm.SetFormalCharge((int)atomCharge); 2023-09-12T10:59:47,530 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T10:59:47,530 ./src/formats/crkformat.cpp:242:30: note: ‘atomCharge’ was declared here 2023-09-12T10:59:47,531 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T10:59:47,531 | ^~~~~~~~~~ 2023-09-12T10:59:47,532 ./src/formats/crkformat.cpp:286:30: warning: ‘atomZ’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,533 286 | atm.SetVector(atomX,atomY,atomZ); 2023-09-12T10:59:47,533 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:47,534 ./src/formats/crkformat.cpp:242:24: note: ‘atomZ’ was declared here 2023-09-12T10:59:47,535 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T10:59:47,535 | ^~~~~ 2023-09-12T10:59:47,536 ./src/formats/crkformat.cpp:286:30: warning: ‘atomY’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,537 286 | atm.SetVector(atomX,atomY,atomZ); 2023-09-12T10:59:47,537 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:47,538 ./src/formats/crkformat.cpp:242:18: note: ‘atomY’ was declared here 2023-09-12T10:59:47,539 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T10:59:47,539 | ^~~~~ 2023-09-12T10:59:47,540 ./src/formats/crkformat.cpp:286:30: warning: ‘atomX’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,541 286 | atm.SetVector(atomX,atomY,atomZ); 2023-09-12T10:59:47,541 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:47,542 ./src/formats/crkformat.cpp:242:12: note: ‘atomX’ was declared here 2023-09-12T10:59:47,542 242 | double atomX,atomY,atomZ,atomCharge; 2023-09-12T10:59:47,543 | ^~~~~ 2023-09-12T10:59:47,543 In member function ‘void OpenBabel::OBAtom::SetAtomicNum(int)’, 2023-09-12T10:59:47,544 inlined from ‘static bool OpenBabel::CRK2DFormat::ReadCRK(std::istream&, OpenBabel::OBMol&, const char*)’ at ./src/formats/crkformat.cpp:285:33: 2023-09-12T10:59:47,544 include/openbabel/atom.h:144:52: warning: ‘atomNumber’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,545 144 | void SetAtomicNum(int atomicnum) { _ele = (char)atomicnum; } 2023-09-12T10:59:47,545 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:47,546 ./src/formats/crkformat.cpp: In static member function ‘static bool OpenBabel::CRK2DFormat::ReadCRK(std::istream&, OpenBabel::OBMol&, const char*)’: 2023-09-12T10:59:47,546 ./src/formats/crkformat.cpp:241:16: note: ‘atomNumber’ was declared here 2023-09-12T10:59:47,547 241 | int atomID,atomNumber; 2023-09-12T10:59:47,547 | ^~~~~~~~~~ 2023-09-12T10:59:47,548 ./src/formats/crkformat.cpp:283:37: warning: ‘atomID’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T10:59:47,549 283 | statomID[numAtoms++]=atomID; 2023-09-12T10:59:47,549 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T10:59:47,550 ./src/formats/crkformat.cpp:241:9: note: ‘atomID’ was declared here 2023-09-12T10:59:47,550 241 | int atomID,atomNumber; 2023-09-12T10:59:47,551 | ^~~~~~ 2023-09-12T10:59:48,402 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/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/' 2023-09-12T10:59:48,403 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/crkformat.o /tmp/ccqZIicb.s 2023-09-12T10:59:48,407 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:48,676 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/ 2023-09-12T10:59:48,676 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/ 2023-09-12T10:59:48,677 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/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.' 2023-09-12T10:59:48,679 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 2023-09-12T10:59:48,682 Using built-in specs. 2023-09-12T10:59:48,683 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:48,684 Target: arm-linux-gnueabihf 2023-09-12T10:59:48,684 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 2023-09-12T10:59:48,685 Thread model: posix 2023-09-12T10:59:48,685 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:48,686 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:48,686 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/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/' 2023-09-12T10:59:48,687 /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/ccFwv8X5.s 2023-09-12T10:59:48,695 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:48,696 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 2023-09-12T10:59:48,697 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:48,698 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:48,699 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:48,699 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:48,700 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:48,700 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:48,701 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:48,702 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:48,702 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:48,703 #include "..." search starts here: 2023-09-12T10:59:48,703 #include <...> search starts here: 2023-09-12T10:59:48,704 /usr/include/eigen3 2023-09-12T10:59:48,704 include 2023-09-12T10:59:48,704 /usr/include/python3.11 2023-09-12T10:59:48,705 /usr/include/c++/12 2023-09-12T10:59:48,705 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:48,706 /usr/include/c++/12/backward 2023-09-12T10:59:48,706 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:48,706 /usr/local/include 2023-09-12T10:59:48,707 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:48,707 /usr/include 2023-09-12T10:59:48,708 End of search list. 2023-09-12T10:59:48,708 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:48,709 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:48,710 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:48,710 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:48,718 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:50,373 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:50,373 from include/openbabel/mol.h:43, 2023-09-12T10:59:50,374 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:50,375 from ./src/formats/crystal09format.cpp:21: 2023-09-12T10:59:50,375 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:50,376 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:50,377 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:50,378 | ^ 2023-09-12T10:59:50,378 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:50,379 37 | # define UNUSED(x) x 2023-09-12T10:59:50,380 | ^ 2023-09-12T10:59:51,072 In file included from include/openbabel/mol.h:52: 2023-09-12T10:59:51,073 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:51,074 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:51,074 862 | {return new OBVibrationData(*this);} 2023-09-12T10:59:51,075 | ^ 2023-09-12T10:59:51,076 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T10:59:51,076 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T10:59:51,077 | ^~~~~~~~ 2023-09-12T10:59:51,078 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:51,079 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:51,080 907 | {return new OBDOSData(*this);} 2023-09-12T10:59:51,080 | ^ 2023-09-12T10:59:51,081 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T10:59:51,082 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T10:59:51,083 | ^~~~~~~~ 2023-09-12T10:59:51,097 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:51,098 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:51,099 954 | {return new OBOrbitalData(*this);} 2023-09-12T10:59:51,099 | ^ 2023-09-12T10:59:51,100 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T10:59:51,100 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T10:59:51,101 | ^~~~~~~~ 2023-09-12T10:59:51,104 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T10:59:51,105 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T10:59:51,105 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T10:59:51,106 | ^ 2023-09-12T10:59:51,107 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T10:59:51,107 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T10:59:51,108 | ^~~~~~~~ 2023-09-12T10:59:51,276 In file included from include/openbabel/format.h:22, 2023-09-12T10:59:51,277 from include/openbabel/obconversion.h:37, 2023-09-12T10:59:51,278 from include/openbabel/obmolecformat.h:31: 2023-09-12T10:59:51,278 include/openbabel/plugin.h: At global scope: 2023-09-12T10:59:51,279 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T10:59:51,280 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T10:59:51,281 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:51,281 In file included from /usr/include/c++/12/string:48, 2023-09-12T10:59:51,282 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T10:59:51,283 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T10:59:51,283 from /usr/include/c++/12/ios:42, 2023-09-12T10:59:51,284 from /usr/include/c++/12/istream:38, 2023-09-12T10:59:51,285 from /usr/include/c++/12/fstream:38, 2023-09-12T10:59:51,285 from ./src/formats/crystal09format.cpp:15: 2023-09-12T10:59:51,286 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T10:59:51,287 131 | struct binary_function 2023-09-12T10:59:51,287 | ^~~~~~~~~~~~~~~ 2023-09-12T10:59:54,390 In file included from /usr/include/c++/12/vector:70, 2023-09-12T10:59:54,390 from ./src/formats/crystal09format.cpp:18: 2023-09-12T10:59:54,391 /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]’: 2023-09-12T10:59:54,392 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:54,393 439 | vector<_Tp, _Alloc>:: 2023-09-12T10:59:54,393 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:54,440 /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]’: 2023-09-12T10:59:54,441 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:54,501 /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]’: 2023-09-12T10:59:54,501 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T10:59:56,294 In file included from /usr/include/c++/12/vector:64: 2023-09-12T10:59:56,295 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:56,296 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:219:25: 2023-09-12T10:59:56,296 /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 2023-09-12T10:59:56,297 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:59:56,297 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:59:56,298 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:56,299 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:220:30: 2023-09-12T10:59:56,300 /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 2023-09-12T10:59:56,301 1287 | _M_realloc_insert(end(), __x); 2023-09-12T10:59:56,301 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T10:59:56,302 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:56,303 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, 2023-09-12T10:59:56,304 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:246:27: 2023-09-12T10:59:56,304 /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 2023-09-12T10:59:56,305 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,305 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,306 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:56,307 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, 2023-09-12T10:59:56,308 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:252:27: 2023-09-12T10:59:56,309 /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 2023-09-12T10:59:56,309 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,310 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,310 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T10:59:56,311 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, 2023-09-12T10:59:56,312 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:258:27: 2023-09-12T10:59:56,312 /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 2023-09-12T10:59:56,313 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,313 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,314 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:56,315 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, 2023-09-12T10:59:56,316 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:261:24: 2023-09-12T10:59:56,317 /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 2023-09-12T10:59:56,318 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,318 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,319 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:56,320 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, 2023-09-12T10:59:56,321 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:262:24: 2023-09-12T10:59:56,322 /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 2023-09-12T10:59:56,322 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,323 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,324 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:56,325 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, 2023-09-12T10:59:56,326 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:263:26: 2023-09-12T10:59:56,327 /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 2023-09-12T10:59:56,327 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,328 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,328 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:56,329 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, 2023-09-12T10:59:56,330 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:264:25: 2023-09-12T10:59:56,330 /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 2023-09-12T10:59:56,331 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,332 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,332 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:56,333 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, 2023-09-12T10:59:56,334 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:265:25: 2023-09-12T10:59:56,335 /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 2023-09-12T10:59:56,335 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,336 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:56,337 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T10:59:56,337 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, 2023-09-12T10:59:56,338 inlined from ‘virtual bool OpenBabel::Crystal09Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/crystal09format.cpp:266:24: 2023-09-12T10:59:56,339 /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 2023-09-12T10:59:56,339 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T10:59:56,340 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T10:59:57,808 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:59:57,809 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/ccFwv8X5.s 2023-09-12T10:59:57,813 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T10:59:58,209 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/ 2023-09-12T10:59:58,210 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/ 2023-09-12T10:59:58,210 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T10:59:58,212 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 2023-09-12T10:59:58,216 Using built-in specs. 2023-09-12T10:59:58,217 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T10:59:58,217 Target: arm-linux-gnueabihf 2023-09-12T10:59:58,218 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 2023-09-12T10:59:58,218 Thread model: posix 2023-09-12T10:59:58,219 Supported LTO compression algorithms: zlib zstd 2023-09-12T10:59:58,219 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T10:59:58,220 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T10:59:58,221 /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/ccchlkuZ.s 2023-09-12T10:59:58,229 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:58,230 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T10:59:58,231 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:58,231 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:58,232 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T10:59:58,232 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T10:59:58,232 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T10:59:58,233 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T10:59:58,234 ignoring duplicate directory "/usr/include/" 2023-09-12T10:59:58,234 as it is a non-system directory that duplicates a system directory 2023-09-12T10:59:58,235 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T10:59:58,235 #include "..." search starts here: 2023-09-12T10:59:58,236 #include <...> search starts here: 2023-09-12T10:59:58,237 /usr/include/eigen3 2023-09-12T10:59:58,237 include 2023-09-12T10:59:58,238 /usr/include/python3.11 2023-09-12T10:59:58,239 /usr/include/c++/12 2023-09-12T10:59:58,239 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T10:59:58,240 /usr/include/c++/12/backward 2023-09-12T10:59:58,240 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T10:59:58,241 /usr/local/include 2023-09-12T10:59:58,242 /usr/include/arm-linux-gnueabihf 2023-09-12T10:59:58,242 /usr/include 2023-09-12T10:59:58,243 End of search list. 2023-09-12T10:59:58,244 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T10:59:58,244 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 2023-09-12T10:59:58,245 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T10:59:58,246 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T10:59:58,249 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T10:59:59,824 In file included from include/openbabel/atom.h:33, 2023-09-12T10:59:59,825 from include/openbabel/mol.h:43, 2023-09-12T10:59:59,825 from include/openbabel/obmolecformat.h:26, 2023-09-12T10:59:59,826 from ./src/formats/cssrformat.cpp:17: 2023-09-12T10:59:59,827 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T10:59:59,827 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T10:59:59,828 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T10:59:59,829 | ^ 2023-09-12T10:59:59,830 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T10:59:59,831 37 | # define UNUSED(x) x 2023-09-12T10:59:59,831 | ^ 2023-09-12T11:00:00,598 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:00,598 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:00,599 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:00,600 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:00,600 | ^ 2023-09-12T11:00:00,601 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:00,601 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:00,602 | ^~~~~~~~ 2023-09-12T11:00:00,604 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:00,604 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:00,605 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:00,605 | ^ 2023-09-12T11:00:00,606 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:00,606 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:00,607 | ^~~~~~~~ 2023-09-12T11:00:00,623 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:00,624 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:00,624 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:00,625 | ^ 2023-09-12T11:00:00,626 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:00,627 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:00,628 | ^~~~~~~~ 2023-09-12T11:00:00,630 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:00,631 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:00,631 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:00,632 | ^ 2023-09-12T11:00:00,633 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:00,633 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:00,634 | ^~~~~~~~ 2023-09-12T11:00:00,803 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:00,804 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:00,805 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:00,805 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:00,806 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:00,806 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:00,807 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:00,807 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:00,808 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:00,808 from include/openbabel/mol.h:35: 2023-09-12T11:00:00,809 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:00,809 131 | struct binary_function 2023-09-12T11:00:00,810 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:04,023 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/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/' 2023-09-12T11:00:04,024 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/ccchlkuZ.s 2023-09-12T11:00:04,030 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:04,228 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/ 2023-09-12T11:00:04,228 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/ 2023-09-12T11:00:04,229 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:00:04,230 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 2023-09-12T11:00:04,235 Using built-in specs. 2023-09-12T11:00:04,235 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:04,236 Target: arm-linux-gnueabihf 2023-09-12T11:00:04,237 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 2023-09-12T11:00:04,237 Thread model: posix 2023-09-12T11:00:04,238 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:04,239 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:04,239 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:04,240 /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/ccQ48ma3.s 2023-09-12T11:00:04,249 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:04,250 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 2023-09-12T11:00:04,252 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:04,252 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:04,253 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:04,254 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:04,254 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:04,255 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:04,256 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:04,257 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:04,257 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:04,258 #include "..." search starts here: 2023-09-12T11:00:04,258 #include <...> search starts here: 2023-09-12T11:00:04,259 /usr/include/eigen3 2023-09-12T11:00:04,260 include 2023-09-12T11:00:04,260 /usr/include/python3.11 2023-09-12T11:00:04,261 /usr/include/c++/12 2023-09-12T11:00:04,262 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:04,262 /usr/include/c++/12/backward 2023-09-12T11:00:04,263 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:04,264 /usr/local/include 2023-09-12T11:00:04,264 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:04,265 /usr/include 2023-09-12T11:00:04,266 End of search list. 2023-09-12T11:00:04,266 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:04,267 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:04,268 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:04,269 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:04,270 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:06,650 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:06,651 from include/openbabel/mol.h:43, 2023-09-12T11:00:06,651 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:06,652 from ./src/formats/daltonformat.cpp:15: 2023-09-12T11:00:06,653 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:06,653 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:06,654 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:06,654 | ^ 2023-09-12T11:00:06,655 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:06,656 37 | # define UNUSED(x) x 2023-09-12T11:00:06,656 | ^ 2023-09-12T11:00:07,429 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:07,430 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:07,430 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:07,431 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:07,432 | ^ 2023-09-12T11:00:07,432 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:07,433 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:07,434 | ^~~~~~~~ 2023-09-12T11:00:07,435 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:07,435 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:07,436 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:07,437 | ^ 2023-09-12T11:00:07,438 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:07,438 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:07,439 | ^~~~~~~~ 2023-09-12T11:00:07,454 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:07,455 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:07,456 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:07,456 | ^ 2023-09-12T11:00:07,457 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:07,458 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:07,459 | ^~~~~~~~ 2023-09-12T11:00:07,461 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:07,462 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:07,462 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:07,463 | ^ 2023-09-12T11:00:07,464 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:07,464 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:07,465 | ^~~~~~~~ 2023-09-12T11:00:07,635 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:07,635 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:07,636 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:07,636 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:07,637 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:07,637 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:07,638 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:07,639 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:07,640 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:07,641 from include/openbabel/mol.h:35: 2023-09-12T11:00:07,641 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:07,642 131 | struct binary_function 2023-09-12T11:00:07,643 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:07,849 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:07,850 ./src/formats/daltonformat.cpp:142:9: warning: variable ‘atomcount’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:00:07,851 142 | int atomcount = 0; // for each atom type 2023-09-12T11:00:07,852 | ^~~~~~~~~ 2023-09-12T11:00:07,857 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:07,858 ./src/formats/daltonformat.cpp:306:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:00:07,859 306 | if(atom->GetAtomicNum() != atomtype) 2023-09-12T11:00:07,860 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T11:00:07,862 ./src/formats/daltonformat.cpp:326:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:00:07,863 326 | if(atom->GetAtomicNum() != atomtype) 2023-09-12T11:00:07,864 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2023-09-12T11:00:11,410 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/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/' 2023-09-12T11:00:11,411 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/ccQ48ma3.s 2023-09-12T11:00:11,415 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:11,658 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/ 2023-09-12T11:00:11,659 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/ 2023-09-12T11:00:11,659 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:00:11,661 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 2023-09-12T11:00:11,665 Using built-in specs. 2023-09-12T11:00:11,666 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:11,666 Target: arm-linux-gnueabihf 2023-09-12T11:00:11,667 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 2023-09-12T11:00:11,667 Thread model: posix 2023-09-12T11:00:11,668 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:11,668 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:11,669 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:11,670 /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/ccU8wOnR.s 2023-09-12T11:00:11,678 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:11,679 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 2023-09-12T11:00:11,680 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:11,680 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:11,681 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:11,681 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:11,682 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:11,682 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:11,683 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:11,683 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:11,684 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:11,684 #include "..." search starts here: 2023-09-12T11:00:11,685 #include <...> search starts here: 2023-09-12T11:00:11,686 /usr/include/eigen3 2023-09-12T11:00:11,686 include 2023-09-12T11:00:11,687 /usr/include/python3.11 2023-09-12T11:00:11,687 /usr/include/c++/12 2023-09-12T11:00:11,688 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:11,689 /usr/include/c++/12/backward 2023-09-12T11:00:11,689 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:11,690 /usr/local/include 2023-09-12T11:00:11,691 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:11,691 /usr/include 2023-09-12T11:00:11,692 End of search list. 2023-09-12T11:00:11,692 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:11,693 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:11,695 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:11,695 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:11,700 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:13,282 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:13,283 from include/openbabel/mol.h:43, 2023-09-12T11:00:13,283 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:13,284 from ./src/formats/dlpolyformat.cpp:14: 2023-09-12T11:00:13,285 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:13,285 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:13,286 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:13,287 | ^ 2023-09-12T11:00:13,288 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:13,288 37 | # define UNUSED(x) x 2023-09-12T11:00:13,289 | ^ 2023-09-12T11:00:14,051 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:14,051 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:14,052 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:14,052 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:14,053 | ^ 2023-09-12T11:00:14,053 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:14,054 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:14,055 | ^~~~~~~~ 2023-09-12T11:00:14,057 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:14,057 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:14,058 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:14,059 | ^ 2023-09-12T11:00:14,059 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:14,060 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:14,061 | ^~~~~~~~ 2023-09-12T11:00:14,077 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:14,078 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:14,078 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:14,079 | ^ 2023-09-12T11:00:14,080 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:14,080 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:14,081 | ^~~~~~~~ 2023-09-12T11:00:14,084 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:14,085 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:14,086 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:14,086 | ^ 2023-09-12T11:00:14,087 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:14,088 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:14,088 | ^~~~~~~~ 2023-09-12T11:00:14,259 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:14,259 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:14,260 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:14,261 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:14,262 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:14,262 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:14,263 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:14,263 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:14,264 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:14,264 from include/openbabel/mol.h:35: 2023-09-12T11:00:14,265 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:14,265 131 | struct binary_function 2023-09-12T11:00:14,266 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:14,697 ./src/formats/dlpolyformat.cpp: In member function ‘bool OpenBabel::DlpolyInputReader::ParseUnitCell(std::istream&, OpenBabel::OBMol&)’: 2023-09-12T11:00:14,697 ./src/formats/dlpolyformat.cpp:147:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:00:14,698 147 | bool ok; 2023-09-12T11:00:14,698 | ^~ 2023-09-12T11:00:20,480 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:00:20,481 /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]’: 2023-09-12T11:00:20,482 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:00:20,482 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:00:20,483 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:20,808 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:00:20,809 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, 2023-09-12T11:00:20,810 inlined from ‘bool OpenBabel::DlpolyInputReader::ReadAtom(std::istream&, OpenBabel::OBMol&)’ at ./src/formats/dlpolyformat.cpp:242:25: 2023-09-12T11:00:20,810 /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 2023-09-12T11:00:20,811 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:00:20,812 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:23,347 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:23,347 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/formats/dlpolyformat.o /tmp/ccU8wOnR.s 2023-09-12T11:00:23,352 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:24,112 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/ 2023-09-12T11:00:24,113 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/ 2023-09-12T11:00:24,114 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:00:24,117 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 2023-09-12T11:00:24,121 Using built-in specs. 2023-09-12T11:00:24,122 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:24,122 Target: arm-linux-gnueabihf 2023-09-12T11:00:24,123 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 2023-09-12T11:00:24,123 Thread model: posix 2023-09-12T11:00:24,124 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:24,124 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:24,125 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:24,125 /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/cc2DXJgz.s 2023-09-12T11:00:24,134 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:24,135 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 2023-09-12T11:00:24,136 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:24,137 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:24,137 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:24,137 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:24,138 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:24,138 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:24,139 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:24,139 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:24,140 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:24,140 #include "..." search starts here: 2023-09-12T11:00:24,140 #include <...> search starts here: 2023-09-12T11:00:24,141 /usr/include/eigen3 2023-09-12T11:00:24,141 include 2023-09-12T11:00:24,142 /usr/include/python3.11 2023-09-12T11:00:24,142 /usr/include/c++/12 2023-09-12T11:00:24,143 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:24,143 /usr/include/c++/12/backward 2023-09-12T11:00:24,144 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:24,144 /usr/local/include 2023-09-12T11:00:24,145 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:24,145 /usr/include 2023-09-12T11:00:24,146 End of search list. 2023-09-12T11:00:24,146 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:24,147 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:24,148 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:24,149 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:24,152 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:25,709 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:25,710 from include/openbabel/mol.h:43, 2023-09-12T11:00:25,710 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:25,711 from ./src/formats/dmolformat.cpp:16: 2023-09-12T11:00:25,712 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:25,713 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:25,713 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:25,714 | ^ 2023-09-12T11:00:25,715 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:25,715 37 | # define UNUSED(x) x 2023-09-12T11:00:25,716 | ^ 2023-09-12T11:00:26,475 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:26,475 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:26,476 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:26,477 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:26,477 | ^ 2023-09-12T11:00:26,478 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:26,479 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:26,480 | ^~~~~~~~ 2023-09-12T11:00:26,481 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:26,481 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:26,482 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:26,483 | ^ 2023-09-12T11:00:26,483 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:26,484 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:26,484 | ^~~~~~~~ 2023-09-12T11:00:26,499 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:26,499 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:26,500 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:26,500 | ^ 2023-09-12T11:00:26,501 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:26,502 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:26,502 | ^~~~~~~~ 2023-09-12T11:00:26,505 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:26,506 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:26,507 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:26,507 | ^ 2023-09-12T11:00:26,508 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:26,509 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:26,510 | ^~~~~~~~ 2023-09-12T11:00:26,677 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:26,678 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:26,678 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:26,679 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:26,680 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:26,680 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:26,681 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:26,682 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:26,683 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:26,683 from include/openbabel/mol.h:35: 2023-09-12T11:00:26,684 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:26,685 131 | struct binary_function 2023-09-12T11:00:26,686 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:29,715 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:29,716 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/cc2DXJgz.s 2023-09-12T11:00:29,720 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:29,925 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/ 2023-09-12T11:00:29,926 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/ 2023-09-12T11:00:29,926 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/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.' 2023-09-12T11:00:29,927 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/exampleformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/exampleformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:00:29,931 Using built-in specs. 2023-09-12T11:00:29,932 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:29,932 Target: arm-linux-gnueabihf 2023-09-12T11:00:29,933 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 2023-09-12T11:00:29,933 Thread model: posix 2023-09-12T11:00:29,934 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:29,935 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:29,935 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/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/' 2023-09-12T11:00:29,936 /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/ccag6szw.s 2023-09-12T11:00:29,944 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:29,945 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 2023-09-12T11:00:29,946 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:29,946 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:29,947 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:29,948 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:29,948 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:29,949 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:29,949 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:29,950 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:29,950 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:29,951 #include "..." search starts here: 2023-09-12T11:00:29,952 #include <...> search starts here: 2023-09-12T11:00:29,952 /usr/include/eigen3 2023-09-12T11:00:29,953 include 2023-09-12T11:00:29,954 /usr/include/python3.11 2023-09-12T11:00:29,954 /usr/include/c++/12 2023-09-12T11:00:29,955 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:29,956 /usr/include/c++/12/backward 2023-09-12T11:00:29,956 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:29,957 /usr/local/include 2023-09-12T11:00:29,957 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:29,958 /usr/include 2023-09-12T11:00:29,958 End of search list. 2023-09-12T11:00:29,959 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:29,960 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 2023-09-12T11:00:29,961 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:29,961 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:29,966 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:30,336 ./src/formats/exampleformat.cpp:178:9: warning: "/*" within comment [-Wcomment] 2023-09-12T11:00:30,336 178 | /* Return true if ok. Returning false means discard the OBMol and stop 2023-09-12T11:00:30,337 | 2023-09-12T11:00:31,557 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:31,558 from include/openbabel/mol.h:43, 2023-09-12T11:00:31,558 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:31,559 from ./src/formats/exampleformat.cpp:34: 2023-09-12T11:00:31,560 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:31,560 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:31,561 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:31,561 | ^ 2023-09-12T11:00:31,562 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:31,563 37 | # define UNUSED(x) x 2023-09-12T11:00:31,563 | ^ 2023-09-12T11:00:32,325 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:32,326 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:32,326 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:32,327 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:32,327 | ^ 2023-09-12T11:00:32,328 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:32,328 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:32,329 | ^~~~~~~~ 2023-09-12T11:00:32,330 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:32,331 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:32,332 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:32,333 | ^ 2023-09-12T11:00:32,333 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:32,334 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:32,335 | ^~~~~~~~ 2023-09-12T11:00:32,349 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:32,350 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:32,351 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:32,351 | ^ 2023-09-12T11:00:32,352 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:32,353 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:32,353 | ^~~~~~~~ 2023-09-12T11:00:32,355 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:32,356 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:32,357 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:32,358 | ^ 2023-09-12T11:00:32,359 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:32,359 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:32,360 | ^~~~~~~~ 2023-09-12T11:00:32,528 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:32,529 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:32,529 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:32,530 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:32,531 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:32,531 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:32,532 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:32,532 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:32,533 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:32,533 from include/openbabel/mol.h:35: 2023-09-12T11:00:32,534 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:32,534 131 | struct binary_function 2023-09-12T11:00:32,535 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:32,729 ./src/formats/exampleformat.cpp: In member function ‘virtual int OpenBabel::XXXFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:00:32,730 ./src/formats/exampleformat.cpp:128:37: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:00:32,731 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:00:32,731 | ~~~~^ 2023-09-12T11:00:32,732 ./src/formats/exampleformat.cpp:128:54: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:00:32,733 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:00:32,734 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:00:32,735 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:32,735 ./src/formats/exampleformat.cpp:156:12: warning: unused variable ‘ifs’ [-Wunused-variable] 2023-09-12T11:00:32,736 156 | istream& ifs = *pConv->GetInStream(); 2023-09-12T11:00:32,737 | ^~~ 2023-09-12T11:00:32,738 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:32,739 ./src/formats/exampleformat.cpp:203:13: warning: variable ‘levels’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:00:32,740 203 | int levels=0; 2023-09-12T11:00:32,740 | ^~~~~~ 2023-09-12T11:00:34,261 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:34,262 ./src/formats/exampleformat.cpp:171:27: warning: ‘dim’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:00:34,263 171 | pmol->SetDimension(dim); 2023-09-12T11:00:34,263 | ~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:00:34,264 ./src/formats/exampleformat.cpp:170:13: note: ‘dim’ was declared here 2023-09-12T11:00:34,265 170 | int dim; 2023-09-12T11:00:34,265 | ^~~ 2023-09-12T11:00:35,026 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:35,026 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/ccag6szw.s 2023-09-12T11:00:35,031 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:35,175 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/ 2023-09-12T11:00:35,175 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/ 2023-09-12T11:00:35,176 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:00:35,177 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 2023-09-12T11:00:35,181 Using built-in specs. 2023-09-12T11:00:35,181 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:35,182 Target: arm-linux-gnueabihf 2023-09-12T11:00:35,183 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 2023-09-12T11:00:35,183 Thread model: posix 2023-09-12T11:00:35,184 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:35,184 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:35,185 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:35,186 /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/ccXTPcWT.s 2023-09-12T11:00:35,194 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:35,195 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:35,196 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:35,196 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:35,197 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:35,197 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:35,197 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:35,198 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:35,199 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:35,199 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:35,200 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:35,201 #include "..." search starts here: 2023-09-12T11:00:35,201 #include <...> search starts here: 2023-09-12T11:00:35,202 /usr/include/eigen3 2023-09-12T11:00:35,203 include 2023-09-12T11:00:35,203 /usr/include/python3.11 2023-09-12T11:00:35,204 /usr/include/c++/12 2023-09-12T11:00:35,205 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:35,205 /usr/include/c++/12/backward 2023-09-12T11:00:35,206 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:35,206 /usr/local/include 2023-09-12T11:00:35,207 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:35,208 /usr/include 2023-09-12T11:00:35,208 End of search list. 2023-09-12T11:00:35,209 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:35,210 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:35,211 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:35,211 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:35,214 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:36,799 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:36,800 from include/openbabel/mol.h:43, 2023-09-12T11:00:36,801 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:36,801 from ./src/formats/exyzformat.cpp:18: 2023-09-12T11:00:36,802 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:36,803 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:36,804 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:36,804 | ^ 2023-09-12T11:00:36,805 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:36,806 37 | # define UNUSED(x) x 2023-09-12T11:00:36,806 | ^ 2023-09-12T11:00:37,575 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:37,576 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:37,576 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:37,577 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:37,577 | ^ 2023-09-12T11:00:37,578 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:37,578 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:37,579 | ^~~~~~~~ 2023-09-12T11:00:37,583 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:37,583 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:37,584 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:37,584 | ^ 2023-09-12T11:00:37,585 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:37,585 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:37,586 | ^~~~~~~~ 2023-09-12T11:00:37,604 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:37,605 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:37,605 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:37,606 | ^ 2023-09-12T11:00:37,607 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:37,608 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:37,608 | ^~~~~~~~ 2023-09-12T11:00:37,613 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:37,613 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:37,614 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:37,615 | ^ 2023-09-12T11:00:37,616 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:37,617 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:37,617 | ^~~~~~~~ 2023-09-12T11:00:37,787 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:37,788 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:37,788 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:37,789 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:37,789 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:37,790 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:37,790 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:37,791 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:37,792 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:37,792 from include/openbabel/mol.h:35: 2023-09-12T11:00:37,793 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:37,793 131 | struct binary_function 2023-09-12T11:00:37,794 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:38,135 ./src/formats/exyzformat.cpp: In member function ‘virtual bool OpenBabel::EXYZFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:00:38,136 ./src/formats/exyzformat.cpp:133:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:00:38,136 133 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2023-09-12T11:00:38,137 | ~^ ~~~~~~~ 2023-09-12T11:00:38,137 | | | 2023-09-12T11:00:38,138 | | unsigned int* 2023-09-12T11:00:38,139 | int* 2023-09-12T11:00:38,140 | %d 2023-09-12T11:00:38,217 ./src/formats/exyzformat.cpp:118:19: warning: variable ‘virtualAtoms’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:00:38,218 118 | bool unitCell,virtualAtoms; 2023-09-12T11:00:38,219 | ^~~~~~~~~~~~ 2023-09-12T11:00:44,017 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/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/' 2023-09-12T11:00:44,018 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/ccXTPcWT.s 2023-09-12T11:00:44,026 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:44,417 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/ 2023-09-12T11:00:44,417 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/ 2023-09-12T11:00:44,418 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:00:44,419 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 2023-09-12T11:00:44,424 Using built-in specs. 2023-09-12T11:00:44,425 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:44,425 Target: arm-linux-gnueabihf 2023-09-12T11:00:44,426 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 2023-09-12T11:00:44,426 Thread model: posix 2023-09-12T11:00:44,427 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:44,427 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:44,428 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:44,428 /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/ccUSlHIv.s 2023-09-12T11:00:44,437 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:44,438 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:44,439 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:44,440 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:44,440 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:44,441 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:44,441 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:44,442 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:44,443 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:44,444 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:44,444 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:44,445 #include "..." search starts here: 2023-09-12T11:00:44,445 #include <...> search starts here: 2023-09-12T11:00:44,446 /usr/include/eigen3 2023-09-12T11:00:44,446 include 2023-09-12T11:00:44,446 /usr/include/python3.11 2023-09-12T11:00:44,447 /usr/include/c++/12 2023-09-12T11:00:44,447 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:44,448 /usr/include/c++/12/backward 2023-09-12T11:00:44,448 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:44,449 /usr/local/include 2023-09-12T11:00:44,449 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:44,450 /usr/include 2023-09-12T11:00:44,450 End of search list. 2023-09-12T11:00:44,451 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:44,451 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:44,452 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:44,453 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:44,460 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:46,076 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:46,077 from include/openbabel/mol.h:43, 2023-09-12T11:00:46,077 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:00:46,078 from ./src/formats/fastaformat.cpp:21: 2023-09-12T11:00:46,079 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:46,079 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:46,080 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:46,081 | ^ 2023-09-12T11:00:46,081 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:46,082 37 | # define UNUSED(x) x 2023-09-12T11:00:46,083 | ^ 2023-09-12T11:00:46,855 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:46,856 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:46,856 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:46,857 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:46,858 | ^ 2023-09-12T11:00:46,858 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:46,859 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:46,860 | ^~~~~~~~ 2023-09-12T11:00:46,861 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:46,862 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:46,862 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:46,863 | ^ 2023-09-12T11:00:46,864 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:46,865 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:46,865 | ^~~~~~~~ 2023-09-12T11:00:46,881 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:46,882 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:46,882 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:46,883 | ^ 2023-09-12T11:00:46,883 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:46,884 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:46,885 | ^~~~~~~~ 2023-09-12T11:00:46,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:46,889 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:46,890 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:46,890 | ^ 2023-09-12T11:00:46,891 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:46,892 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:46,893 | ^~~~~~~~ 2023-09-12T11:00:47,061 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:47,062 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:47,063 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:00:47,064 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:47,064 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:47,065 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:47,066 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:47,067 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:00:47,067 from /usr/include/c++/12/vector:66, 2023-09-12T11:00:47,068 from include/openbabel/mol.h:35: 2023-09-12T11:00:47,069 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:47,069 131 | struct binary_function 2023-09-12T11:00:47,070 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:47,335 ./src/formats/fastaformat.cpp: In function ‘void OpenBabel::add_residue(OBMol*, OBResidue*, double, double, long unsigned int&, ResidueRecord*, int, OBAtom*&, bool, bool)’: 2023-09-12T11:00:47,336 ./src/formats/fastaformat.cpp:387:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T11:00:47,337 387 | else if (atom_count > resBondFromOffset) 2023-09-12T11:00:47,337 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:51,169 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/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/' 2023-09-12T11:00:51,170 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/ccUSlHIv.s 2023-09-12T11:00:51,174 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:00:51,473 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/ 2023-09-12T11:00:51,474 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/ 2023-09-12T11:00:51,474 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:00:51,476 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 2023-09-12T11:00:51,480 Using built-in specs. 2023-09-12T11:00:51,481 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:00:51,482 Target: arm-linux-gnueabihf 2023-09-12T11:00:51,482 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 2023-09-12T11:00:51,483 Thread model: posix 2023-09-12T11:00:51,484 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:00:51,484 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:00:51,485 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:00:51,485 /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/ccEIRACQ.s 2023-09-12T11:00:51,494 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:51,495 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:51,495 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:51,496 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:51,496 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:00:51,497 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:00:51,497 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:00:51,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:00:51,499 ignoring duplicate directory "/usr/include/" 2023-09-12T11:00:51,500 as it is a non-system directory that duplicates a system directory 2023-09-12T11:00:51,500 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:00:51,501 #include "..." search starts here: 2023-09-12T11:00:51,501 #include <...> search starts here: 2023-09-12T11:00:51,502 /usr/include/eigen3 2023-09-12T11:00:51,503 include 2023-09-12T11:00:51,503 /usr/include/python3.11 2023-09-12T11:00:51,504 /usr/include/c++/12 2023-09-12T11:00:51,504 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:00:51,505 /usr/include/c++/12/backward 2023-09-12T11:00:51,506 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:00:51,506 /usr/local/include 2023-09-12T11:00:51,507 /usr/include/arm-linux-gnueabihf 2023-09-12T11:00:51,508 /usr/include 2023-09-12T11:00:51,508 End of search list. 2023-09-12T11:00:51,509 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:00:51,509 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:00:51,510 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:00:51,511 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:00:51,512 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:00:53,050 In file included from include/openbabel/atom.h:33, 2023-09-12T11:00:53,051 from include/openbabel/mol.h:43, 2023-09-12T11:00:53,052 from ./src/formats/fastsearchformat.cpp:20: 2023-09-12T11:00:53,052 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:00:53,053 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:00:53,054 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:00:53,055 | ^ 2023-09-12T11:00:53,056 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:00:53,056 37 | # define UNUSED(x) x 2023-09-12T11:00:53,057 | ^ 2023-09-12T11:00:53,822 In file included from include/openbabel/mol.h:52: 2023-09-12T11:00:53,822 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:53,823 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:53,824 862 | {return new OBVibrationData(*this);} 2023-09-12T11:00:53,824 | ^ 2023-09-12T11:00:53,825 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:00:53,825 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:00:53,826 | ^~~~~~~~ 2023-09-12T11:00:53,827 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:53,828 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:53,828 907 | {return new OBDOSData(*this);} 2023-09-12T11:00:53,829 | ^ 2023-09-12T11:00:53,830 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:00:53,831 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:00:53,831 | ^~~~~~~~ 2023-09-12T11:00:53,846 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:53,847 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:53,848 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:00:53,848 | ^ 2023-09-12T11:00:53,849 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:00:53,850 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:00:53,851 | ^~~~~~~~ 2023-09-12T11:00:53,852 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:00:53,853 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:00:53,854 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:00:53,854 | ^ 2023-09-12T11:00:53,855 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:00:53,856 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:00:53,857 | ^~~~~~~~ 2023-09-12T11:00:54,025 In file included from include/openbabel/format.h:22, 2023-09-12T11:00:54,026 from include/openbabel/obconversion.h:37, 2023-09-12T11:00:54,026 from ./src/formats/fastsearchformat.cpp:21: 2023-09-12T11:00:54,027 include/openbabel/plugin.h: At global scope: 2023-09-12T11:00:54,028 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:00:54,028 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:00:54,029 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:54,029 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:00:54,030 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:00:54,030 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:00:54,031 from /usr/include/c++/12/ios:42, 2023-09-12T11:00:54,031 from /usr/include/c++/12/istream:38, 2023-09-12T11:00:54,032 from /usr/include/c++/12/sstream:38, 2023-09-12T11:00:54,032 from ./src/formats/fastsearchformat.cpp:16: 2023-09-12T11:00:54,033 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:00:54,033 131 | struct binary_function 2023-09-12T11:00:54,034 | ^~~~~~~~~~~~~~~ 2023-09-12T11:00:54,316 ./src/formats/fastsearchformat.cpp: In member function ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’: 2023-09-12T11:00:54,317 ./src/formats/fastsearchformat.cpp:652:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:00:54,318 652 | if(idx>=patternMol.NumBonds()) 2023-09-12T11:00:54,318 | ~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:58,871 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:00:58,872 from include/openbabel/mol.h:35: 2023-09-12T11:00:58,872 /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]’: 2023-09-12T11:00:58,873 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:00:58,874 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:00:58,875 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:00:59,006 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:00:59,007 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:00:59,008 inlined from ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’ at ./src/formats/fastsearchformat.cpp:657:28: 2023-09-12T11:00:59,008 /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 2023-09-12T11:00:59,009 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:00:59,010 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:00:59,010 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:00:59,011 inlined from ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’ at ./src/formats/fastsearchformat.cpp:660:28: 2023-09-12T11:00:59,012 /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 2023-09-12T11:00:59,013 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:00:59,013 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:00:59,249 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:00:59,250 inlined from ‘bool OpenBabel::FastSearchFormat::ObtainTarget(OpenBabel::OBConversion*, std::vector&, const std::string&)’ at ./src/formats/fastsearchformat.cpp:606:30: 2023-09-12T11:00:59,251 /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 2023-09-12T11:00:59,251 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:00:59,252 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:00:59,252 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:00:59,253 inlined from ‘bool OpenBabel::FastSearchFormat::ObtainTarget(OpenBabel::OBConversion*, std::vector&, const std::string&)’ at ./src/formats/fastsearchformat.cpp:608:32: 2023-09-12T11:00:59,253 /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 2023-09-12T11:00:59,254 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:00:59,255 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:00:59,255 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:00:59,256 inlined from ‘bool OpenBabel::FastSearchFormat::ObtainTarget(OpenBabel::OBConversion*, std::vector&, const std::string&)’ at ./src/formats/fastsearchformat.cpp:641:26: 2023-09-12T11:00:59,257 /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 2023-09-12T11:00:59,258 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:00:59,259 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:01:00,277 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:01:00,278 inlined from ‘virtual bool OpenBabel::FastSearchFormat::ReadChemObject(OpenBabel::OBConversion*)’ at ./src/formats/fastsearchformat.cpp:212:37: 2023-09-12T11:01:00,278 /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 2023-09-12T11:01:00,279 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:01:00,280 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:01:01,911 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/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/' 2023-09-12T11:01:01,911 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/ccEIRACQ.s 2023-09-12T11:01:01,916 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:02,553 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/ 2023-09-12T11:01:02,554 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/ 2023-09-12T11:01:02,554 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:01:02,558 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 2023-09-12T11:01:02,562 Using built-in specs. 2023-09-12T11:01:02,563 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:02,564 Target: arm-linux-gnueabihf 2023-09-12T11:01:02,564 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 2023-09-12T11:01:02,565 Thread model: posix 2023-09-12T11:01:02,565 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:02,566 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:02,567 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:02,568 /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/ccKVNaiI.s 2023-09-12T11:01:02,576 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:02,577 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:02,578 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:02,578 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:02,579 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:02,579 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:02,580 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:02,580 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:02,581 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:02,581 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:02,582 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:02,582 #include "..." search starts here: 2023-09-12T11:01:02,583 #include <...> search starts here: 2023-09-12T11:01:02,583 /usr/include/eigen3 2023-09-12T11:01:02,584 include 2023-09-12T11:01:02,584 /usr/include/python3.11 2023-09-12T11:01:02,585 /usr/include/c++/12 2023-09-12T11:01:02,586 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:02,586 /usr/include/c++/12/backward 2023-09-12T11:01:02,587 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:02,587 /usr/local/include 2023-09-12T11:01:02,588 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:02,589 /usr/include 2023-09-12T11:01:02,589 End of search list. 2023-09-12T11:01:02,590 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:02,591 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 2023-09-12T11:01:02,592 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:02,593 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:02,594 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:04,220 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:04,221 from include/openbabel/mol.h:43, 2023-09-12T11:01:04,222 from ./src/formats/fchkformat.cpp:21: 2023-09-12T11:01:04,222 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:04,223 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:04,224 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:04,224 | ^ 2023-09-12T11:01:04,225 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:04,226 37 | # define UNUSED(x) x 2023-09-12T11:01:04,226 | ^ 2023-09-12T11:01:04,994 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:04,995 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:04,996 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:04,997 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:04,997 | ^ 2023-09-12T11:01:04,998 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:04,999 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:04,999 | ^~~~~~~~ 2023-09-12T11:01:05,001 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:05,001 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:05,002 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:05,002 | ^ 2023-09-12T11:01:05,003 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:05,004 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:05,004 | ^~~~~~~~ 2023-09-12T11:01:05,020 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:05,021 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:05,021 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:05,022 | ^ 2023-09-12T11:01:05,023 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:05,024 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:05,024 | ^~~~~~~~ 2023-09-12T11:01:05,027 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:05,027 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:05,028 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:05,029 | ^ 2023-09-12T11:01:05,029 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:05,030 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:05,031 | ^~~~~~~~ 2023-09-12T11:01:05,200 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:05,201 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:05,201 from ./src/formats/fchkformat.cpp:22: 2023-09-12T11:01:05,202 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:05,203 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:05,203 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:05,204 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:05,205 In file included from /usr/include/c++/12/functional:49, 2023-09-12T11:01:05,206 from ./src/formats/fchkformat.cpp:16: 2023-09-12T11:01:05,206 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:05,207 131 | struct binary_function 2023-09-12T11:01:05,207 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:05,436 ./src/formats/fchkformat.cpp: In member function ‘virtual bool OpenBabel::FCHKFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:01:05,437 ./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] 2023-09-12T11:01:05,437 587 | if (alphaorb_found && (numAOrb > alphaorb.size())) 2023-09-12T11:01:05,438 | ~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:01:05,439 ./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] 2023-09-12T11:01:05,439 600 | if (betaorb_found && (numBOrb > betaorb.size())) 2023-09-12T11:01:05,440 | ~~~~~~~~^~~~~~~~~~~~~~~~ 2023-09-12T11:01:05,444 ./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] 2023-09-12T11:01:05,444 659 | bind2nd(less_equal(), 0)) || 2023-09-12T11:01:05,445 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:05,446 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T11:01:05,447 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:01:05,447 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:01:05,448 | ^~~~~~~ 2023-09-12T11:01:05,449 ./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] 2023-09-12T11:01:05,449 662 | bind2nd(greater(), MxBond)) || 2023-09-12T11:01:05,450 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:05,451 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:01:05,452 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:01:05,452 | ^~~~~~~ 2023-09-12T11:01:05,453 ./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] 2023-09-12T11:01:05,454 665 | bind2nd(less(), 0)) || 2023-09-12T11:01:05,454 | ~~~~~~~^~~~~~~~~~~~~~~~ 2023-09-12T11:01:05,455 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:01:05,456 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:01:05,456 | ^~~~~~~ 2023-09-12T11:01:05,457 ./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] 2023-09-12T11:01:05,458 668 | bind2nd(greater(), Natoms))) 2023-09-12T11:01:05,459 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:05,459 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:01:05,460 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:01:05,461 | ^~~~~~~ 2023-09-12T11:01:05,462 ./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] 2023-09-12T11:01:05,462 691 | if (numAOrb > 0 && alphaorb.size() == numAOrb) { 2023-09-12T11:01:05,463 | ~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:01:05,463 ./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] 2023-09-12T11:01:05,464 695 | if (numBOrb > 0 && betaorb.size() == numBOrb) { // open shell calculation 2023-09-12T11:01:05,464 | ~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:01:09,268 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:01:09,269 from include/openbabel/mol.h:35: 2023-09-12T11:01:09,270 /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]’: 2023-09-12T11:01:09,270 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:01:09,271 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:01:09,271 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:09,383 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:01:09,384 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:01:09,385 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: 2023-09-12T11:01:09,385 /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 2023-09-12T11:01:09,386 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:01:09,387 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:01:09,388 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:01:09,389 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: 2023-09-12T11:01:09,390 /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 2023-09-12T11:01:09,391 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:01:09,392 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:01:11,790 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:01:11,790 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, 2023-09-12T11:01:11,791 inlined from ‘virtual bool OpenBabel::FCHKFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/fchkformat.cpp:231:42: 2023-09-12T11:01:11,792 /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 2023-09-12T11:01:11,792 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:01:11,793 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:01:14,366 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:14,367 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/ccKVNaiI.s 2023-09-12T11:01:14,371 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:15,021 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/ 2023-09-12T11:01:15,022 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/ 2023-09-12T11:01:15,022 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/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.' 2023-09-12T11:01:15,026 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 2023-09-12T11:01:15,030 Using built-in specs. 2023-09-12T11:01:15,031 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:15,032 Target: arm-linux-gnueabihf 2023-09-12T11:01:15,032 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 2023-09-12T11:01:15,033 Thread model: posix 2023-09-12T11:01:15,033 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:15,034 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:15,035 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:15,035 /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/ccz9WCCv.s 2023-09-12T11:01:15,044 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:15,045 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:15,046 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:15,046 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:15,047 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:15,048 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:15,048 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:15,049 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:15,051 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:15,052 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:15,052 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:15,053 #include "..." search starts here: 2023-09-12T11:01:15,054 #include <...> search starts here: 2023-09-12T11:01:15,054 /usr/include/eigen3 2023-09-12T11:01:15,055 include 2023-09-12T11:01:15,055 /usr/include/python3.11 2023-09-12T11:01:15,056 /usr/include/c++/12 2023-09-12T11:01:15,057 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:15,057 /usr/include/c++/12/backward 2023-09-12T11:01:15,058 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:15,059 /usr/local/include 2023-09-12T11:01:15,059 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:15,060 /usr/include 2023-09-12T11:01:15,061 End of search list. 2023-09-12T11:01:15,061 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:15,062 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:15,063 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:15,064 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:15,064 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:16,626 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:16,627 from include/openbabel/mol.h:43, 2023-09-12T11:01:16,628 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:16,628 from ./src/formats/featformat.cpp:17: 2023-09-12T11:01:16,629 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:16,630 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:16,631 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:16,632 | ^ 2023-09-12T11:01:16,633 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:16,633 37 | # define UNUSED(x) x 2023-09-12T11:01:16,634 | ^ 2023-09-12T11:01:17,395 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:17,396 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:17,396 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:17,397 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:17,397 | ^ 2023-09-12T11:01:17,398 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:17,398 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:17,399 | ^~~~~~~~ 2023-09-12T11:01:17,400 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:17,401 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:17,401 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:17,402 | ^ 2023-09-12T11:01:17,403 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:17,404 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:17,404 | ^~~~~~~~ 2023-09-12T11:01:17,419 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:17,420 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:17,421 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:17,421 | ^ 2023-09-12T11:01:17,422 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:17,423 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:17,424 | ^~~~~~~~ 2023-09-12T11:01:17,426 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:17,426 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:17,427 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:17,427 | ^ 2023-09-12T11:01:17,428 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:17,429 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:17,430 | ^~~~~~~~ 2023-09-12T11:01:17,599 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:17,599 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:17,600 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:17,600 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:17,601 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:17,601 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:17,602 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:17,602 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:17,603 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:17,603 from include/openbabel/mol.h:35: 2023-09-12T11:01:17,604 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:17,604 131 | struct binary_function 2023-09-12T11:01:17,605 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:20,165 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:20,166 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/ccz9WCCv.s 2023-09-12T11:01:20,171 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:20,322 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/ 2023-09-12T11:01:20,322 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/ 2023-09-12T11:01:20,323 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/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.' 2023-09-12T11:01:20,324 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 2023-09-12T11:01:20,328 Using built-in specs. 2023-09-12T11:01:20,329 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:20,330 Target: arm-linux-gnueabihf 2023-09-12T11:01:20,330 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 2023-09-12T11:01:20,331 Thread model: posix 2023-09-12T11:01:20,332 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:20,332 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:20,333 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/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/' 2023-09-12T11:01:20,333 /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/cc6G6ZJq.s 2023-09-12T11:01:20,342 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:20,342 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:20,344 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:20,344 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:20,345 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:20,345 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:20,346 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:20,347 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:20,347 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:20,348 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:20,348 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:20,349 #include "..." search starts here: 2023-09-12T11:01:20,350 #include <...> search starts here: 2023-09-12T11:01:20,350 /usr/include/eigen3 2023-09-12T11:01:20,351 include 2023-09-12T11:01:20,352 /usr/include/python3.11 2023-09-12T11:01:20,352 /usr/include/c++/12 2023-09-12T11:01:20,353 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:20,354 /usr/include/c++/12/backward 2023-09-12T11:01:20,354 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:20,355 /usr/local/include 2023-09-12T11:01:20,356 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:20,356 /usr/include 2023-09-12T11:01:20,357 End of search list. 2023-09-12T11:01:20,358 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:20,358 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:20,359 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:20,360 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:20,360 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:21,948 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:21,948 from include/openbabel/mol.h:43, 2023-09-12T11:01:21,949 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:21,950 from ./src/formats/fhformat.cpp:17: 2023-09-12T11:01:21,950 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:21,951 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:21,951 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:21,952 | ^ 2023-09-12T11:01:21,952 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:21,953 37 | # define UNUSED(x) x 2023-09-12T11:01:21,953 | ^ 2023-09-12T11:01:22,714 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:22,715 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:22,716 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:22,717 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:22,717 | ^ 2023-09-12T11:01:22,718 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:22,719 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:22,720 | ^~~~~~~~ 2023-09-12T11:01:22,720 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:22,721 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:22,722 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:22,723 | ^ 2023-09-12T11:01:22,723 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:22,724 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:22,725 | ^~~~~~~~ 2023-09-12T11:01:22,739 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:22,739 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:22,740 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:22,741 | ^ 2023-09-12T11:01:22,742 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:22,743 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:22,743 | ^~~~~~~~ 2023-09-12T11:01:22,745 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:22,746 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:22,746 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:22,747 | ^ 2023-09-12T11:01:22,747 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:22,748 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:22,748 | ^~~~~~~~ 2023-09-12T11:01:22,919 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:22,919 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:22,920 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:22,920 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:22,921 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:22,922 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:22,922 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:22,923 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:22,924 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:22,924 from include/openbabel/mol.h:35: 2023-09-12T11:01:22,925 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:22,926 131 | struct binary_function 2023-09-12T11:01:22,927 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:25,490 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/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/' 2023-09-12T11:01:25,491 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/fhformat.o /tmp/cc6G6ZJq.s 2023-09-12T11:01:25,495 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:25,645 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/ 2023-09-12T11:01:25,645 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/ 2023-09-12T11:01:25,647 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/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.' 2023-09-12T11:01:25,647 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/fhiaimsformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fhiaimsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:25,651 Using built-in specs. 2023-09-12T11:01:25,652 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:25,653 Target: arm-linux-gnueabihf 2023-09-12T11:01:25,653 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 2023-09-12T11:01:25,654 Thread model: posix 2023-09-12T11:01:25,654 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:25,655 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:25,656 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/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/' 2023-09-12T11:01:25,656 /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/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/ccEbAlIe.s 2023-09-12T11:01:25,665 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:25,666 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 2023-09-12T11:01:25,667 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:25,668 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:25,668 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:25,669 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:25,670 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:25,671 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:25,671 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:25,671 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:25,672 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:25,672 #include "..." search starts here: 2023-09-12T11:01:25,673 #include <...> search starts here: 2023-09-12T11:01:25,673 /usr/include/eigen3 2023-09-12T11:01:25,674 include 2023-09-12T11:01:25,674 /usr/include/python3.11 2023-09-12T11:01:25,674 /usr/include/c++/12 2023-09-12T11:01:25,675 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:25,675 /usr/include/c++/12/backward 2023-09-12T11:01:25,676 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:25,676 /usr/local/include 2023-09-12T11:01:25,677 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:25,677 /usr/include 2023-09-12T11:01:25,678 End of search list. 2023-09-12T11:01:25,678 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:25,679 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 2023-09-12T11:01:25,680 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:25,680 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:25,683 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:27,255 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:27,256 from include/openbabel/mol.h:43, 2023-09-12T11:01:27,256 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:27,257 from ./src/formats/fhiaimsformat.cpp:15: 2023-09-12T11:01:27,258 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:27,258 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:27,259 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:27,260 | ^ 2023-09-12T11:01:27,261 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:27,261 37 | # define UNUSED(x) x 2023-09-12T11:01:27,262 | ^ 2023-09-12T11:01:28,024 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:28,025 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:28,025 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:28,026 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:28,026 | ^ 2023-09-12T11:01:28,027 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:28,028 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:28,029 | ^~~~~~~~ 2023-09-12T11:01:28,029 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:28,030 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:28,031 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:28,032 | ^ 2023-09-12T11:01:28,032 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:28,033 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:28,033 | ^~~~~~~~ 2023-09-12T11:01:28,048 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:28,049 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:28,049 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:28,050 | ^ 2023-09-12T11:01:28,050 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:28,051 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:28,051 | ^~~~~~~~ 2023-09-12T11:01:28,054 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:28,055 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:28,055 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:28,056 | ^ 2023-09-12T11:01:28,057 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:28,057 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:28,058 | ^~~~~~~~ 2023-09-12T11:01:28,226 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:28,227 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:28,228 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:28,229 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:28,229 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:28,230 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:28,231 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:28,231 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:28,232 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:28,233 from include/openbabel/mol.h:35: 2023-09-12T11:01:28,233 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:28,234 131 | struct binary_function 2023-09-12T11:01:28,235 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:30,820 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:01:30,821 /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]’: 2023-09-12T11:01:30,822 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:01:30,823 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:01:30,823 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:30,941 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:01:30,942 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, 2023-09-12T11:01:30,943 inlined from ‘virtual bool OpenBabel::FHIaimsFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/fhiaimsformat.cpp:110:26: 2023-09-12T11:01:30,943 /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 2023-09-12T11:01:30,944 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:01:30,944 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:31,234 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:31,235 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/ccEbAlIe.s 2023-09-12T11:01:31,239 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:31,427 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/ 2023-09-12T11:01:31,428 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/ 2023-09-12T11:01:31,429 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/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.' 2023-09-12T11:01:31,430 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 2023-09-12T11:01:31,434 Using built-in specs. 2023-09-12T11:01:31,435 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:31,436 Target: arm-linux-gnueabihf 2023-09-12T11:01:31,436 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 2023-09-12T11:01:31,437 Thread model: posix 2023-09-12T11:01:31,438 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:31,438 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:31,439 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/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/' 2023-09-12T11:01:31,439 /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/cckRzAQX.s 2023-09-12T11:01:31,448 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:31,449 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:31,450 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:31,450 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:31,451 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:31,452 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:31,452 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:31,453 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:31,453 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:31,454 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:31,455 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:31,455 #include "..." search starts here: 2023-09-12T11:01:31,456 #include <...> search starts here: 2023-09-12T11:01:31,456 /usr/include/eigen3 2023-09-12T11:01:31,457 include 2023-09-12T11:01:31,458 /usr/include/python3.11 2023-09-12T11:01:31,458 /usr/include/c++/12 2023-09-12T11:01:31,459 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:31,460 /usr/include/c++/12/backward 2023-09-12T11:01:31,460 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:31,461 /usr/local/include 2023-09-12T11:01:31,462 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:31,463 /usr/include 2023-09-12T11:01:31,463 End of search list. 2023-09-12T11:01:31,463 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:31,464 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:31,465 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:31,465 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:31,467 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:33,151 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:33,152 from include/openbabel/mol.h:43, 2023-09-12T11:01:33,152 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:33,153 from ./src/formats/fingerprintformat.cpp:19: 2023-09-12T11:01:33,153 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:33,154 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:33,155 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:33,155 | ^ 2023-09-12T11:01:33,156 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:33,156 37 | # define UNUSED(x) x 2023-09-12T11:01:33,157 | ^ 2023-09-12T11:01:33,918 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:33,919 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:33,919 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:33,920 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:33,921 | ^ 2023-09-12T11:01:33,921 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:33,922 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:33,923 | ^~~~~~~~ 2023-09-12T11:01:33,924 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:33,924 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:33,925 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:33,926 | ^ 2023-09-12T11:01:33,926 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:33,927 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:33,928 | ^~~~~~~~ 2023-09-12T11:01:33,942 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:33,943 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:33,944 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:33,944 | ^ 2023-09-12T11:01:33,945 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:33,946 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:33,946 | ^~~~~~~~ 2023-09-12T11:01:33,949 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:33,949 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:33,950 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:33,950 | ^ 2023-09-12T11:01:33,951 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:33,951 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:33,952 | ^~~~~~~~ 2023-09-12T11:01:34,121 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:34,121 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:34,122 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:34,122 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:34,123 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:34,124 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:34,124 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:34,125 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:34,125 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:34,126 from ./src/formats/fingerprintformat.cpp:15: 2023-09-12T11:01:34,127 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:34,128 131 | struct binary_function 2023-09-12T11:01:34,128 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:37,855 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:37,856 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/cckRzAQX.s 2023-09-12T11:01:37,860 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:38,129 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/ 2023-09-12T11:01:38,130 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/ 2023-09-12T11:01:38,131 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/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.' 2023-09-12T11:01:38,132 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/fpsformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/fpsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:38,136 Using built-in specs. 2023-09-12T11:01:38,137 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:38,137 Target: arm-linux-gnueabihf 2023-09-12T11:01:38,138 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 2023-09-12T11:01:38,138 Thread model: posix 2023-09-12T11:01:38,139 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:38,139 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:38,140 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/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/' 2023-09-12T11:01:38,140 /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/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/ccIaBQz9.s 2023-09-12T11:01:38,149 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:38,150 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 2023-09-12T11:01:38,151 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:38,152 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:38,153 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:38,153 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:38,154 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:38,154 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:38,154 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:38,155 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:38,155 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:38,156 #include "..." search starts here: 2023-09-12T11:01:38,156 #include <...> search starts here: 2023-09-12T11:01:38,157 /usr/include/eigen3 2023-09-12T11:01:38,157 include 2023-09-12T11:01:38,157 /usr/include/python3.11 2023-09-12T11:01:38,158 /usr/include/c++/12 2023-09-12T11:01:38,158 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:38,159 /usr/include/c++/12/backward 2023-09-12T11:01:38,159 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:38,160 /usr/local/include 2023-09-12T11:01:38,160 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:38,160 /usr/include 2023-09-12T11:01:38,161 End of search list. 2023-09-12T11:01:38,161 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:38,162 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 2023-09-12T11:01:38,163 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:38,163 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:38,169 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:39,872 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:39,873 from include/openbabel/mol.h:43, 2023-09-12T11:01:39,874 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:39,875 from ./src/formats/fpsformat.cpp:19: 2023-09-12T11:01:39,875 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:39,876 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:39,877 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:39,878 | ^ 2023-09-12T11:01:39,878 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:39,879 37 | # define UNUSED(x) x 2023-09-12T11:01:39,880 | ^ 2023-09-12T11:01:40,645 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:40,646 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:40,647 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:40,647 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:40,648 | ^ 2023-09-12T11:01:40,649 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:40,650 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:40,650 | ^~~~~~~~ 2023-09-12T11:01:40,651 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:40,652 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:40,653 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:40,653 | ^ 2023-09-12T11:01:40,654 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:40,654 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:40,655 | ^~~~~~~~ 2023-09-12T11:01:40,674 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:40,674 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:40,675 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:40,675 | ^ 2023-09-12T11:01:40,676 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:40,677 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:40,677 | ^~~~~~~~ 2023-09-12T11:01:40,681 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:40,682 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:40,683 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:40,683 | ^ 2023-09-12T11:01:40,684 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:40,685 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:40,685 | ^~~~~~~~ 2023-09-12T11:01:40,855 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:40,856 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:40,856 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:40,857 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:40,858 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:40,858 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:40,859 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:40,860 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:40,861 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:40,861 from ./src/formats/fpsformat.cpp:15: 2023-09-12T11:01:40,862 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:40,863 131 | struct binary_function 2023-09-12T11:01:40,864 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:41,082 ./src/formats/fpsformat.cpp: In member function ‘virtual bool OpenBabel::FPSFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:01:41,083 ./src/formats/fpsformat.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:01:41,084 146 | for(unsigned i=0;i<(_nbits+31)/32;++i) 2023-09-12T11:01:41,084 | ~^~~~~~~~~~~~~~~ 2023-09-12T11:01:41,090 ./src/formats/fpsformat.cpp: In member function ‘std::string OpenBabel::FPSFormat::getTimeStr()’: 2023-09-12T11:01:41,091 ./src/formats/fpsformat.cpp:169:10: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:01:41,092 169 | size_t time_res; /* Result of strftime */ 2023-09-12T11:01:41,092 | ^~~~~~~~ 2023-09-12T11:01:44,456 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:44,457 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/ccIaBQz9.s 2023-09-12T11:01:44,465 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:44,704 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/ 2023-09-12T11:01:44,704 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/ 2023-09-12T11:01:44,705 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/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.' 2023-09-12T11:01:44,706 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/freefracformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/freefracformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:01:44,710 Using built-in specs. 2023-09-12T11:01:44,711 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:44,712 Target: arm-linux-gnueabihf 2023-09-12T11:01:44,712 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 2023-09-12T11:01:44,713 Thread model: posix 2023-09-12T11:01:44,714 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:44,714 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:44,715 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:44,715 /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/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/ccx8X8Yp.s 2023-09-12T11:01:44,724 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:44,725 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 2023-09-12T11:01:44,726 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:44,726 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:44,727 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:44,727 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:44,728 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:44,728 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:44,729 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:44,730 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:44,730 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:44,731 #include "..." search starts here: 2023-09-12T11:01:44,731 #include <...> search starts here: 2023-09-12T11:01:44,732 /usr/include/eigen3 2023-09-12T11:01:44,732 include 2023-09-12T11:01:44,733 /usr/include/python3.11 2023-09-12T11:01:44,733 /usr/include/c++/12 2023-09-12T11:01:44,734 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:44,735 /usr/include/c++/12/backward 2023-09-12T11:01:44,735 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:44,736 /usr/local/include 2023-09-12T11:01:44,736 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:44,737 /usr/include 2023-09-12T11:01:44,737 End of search list. 2023-09-12T11:01:44,738 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:44,739 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 2023-09-12T11:01:44,740 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:44,741 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:44,743 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:46,338 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:46,338 from include/openbabel/mol.h:43, 2023-09-12T11:01:46,339 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:46,339 from ./src/formats/freefracformat.cpp:16: 2023-09-12T11:01:46,340 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:46,341 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:46,341 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:46,342 | ^ 2023-09-12T11:01:46,342 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:46,343 37 | # define UNUSED(x) x 2023-09-12T11:01:46,343 | ^ 2023-09-12T11:01:47,106 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:47,106 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:47,107 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:47,107 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:47,108 | ^ 2023-09-12T11:01:47,109 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:47,110 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:47,111 | ^~~~~~~~ 2023-09-12T11:01:47,111 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:47,112 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:47,113 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:47,113 | ^ 2023-09-12T11:01:47,114 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:47,115 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:47,116 | ^~~~~~~~ 2023-09-12T11:01:47,130 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:47,131 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:47,131 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:47,132 | ^ 2023-09-12T11:01:47,133 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:47,134 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:47,134 | ^~~~~~~~ 2023-09-12T11:01:47,136 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:47,137 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:47,138 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:47,139 | ^ 2023-09-12T11:01:47,140 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:47,140 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:47,141 | ^~~~~~~~ 2023-09-12T11:01:47,309 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:47,310 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:47,310 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:47,311 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:47,311 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:47,312 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:47,312 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:47,313 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:47,314 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:47,315 from include/openbabel/mol.h:35: 2023-09-12T11:01:47,315 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:47,316 131 | struct binary_function 2023-09-12T11:01:47,317 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:50,318 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:01:50,319 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/ccx8X8Yp.s 2023-09-12T11:01:50,323 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:01:50,527 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/ 2023-09-12T11:01:50,528 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/ 2023-09-12T11:01:50,528 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/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.' 2023-09-12T11:01:50,530 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 2023-09-12T11:01:50,533 Using built-in specs. 2023-09-12T11:01:50,534 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:01:50,535 Target: arm-linux-gnueabihf 2023-09-12T11:01:50,535 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 2023-09-12T11:01:50,536 Thread model: posix 2023-09-12T11:01:50,536 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:01:50,537 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:01:50,537 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/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/' 2023-09-12T11:01:50,538 /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/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/ccrla0GF.s 2023-09-12T11:01:50,547 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:50,547 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 2023-09-12T11:01:50,548 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:50,549 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:50,550 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:01:50,550 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:01:50,551 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:01:50,551 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:01:50,552 ignoring duplicate directory "/usr/include/" 2023-09-12T11:01:50,553 as it is a non-system directory that duplicates a system directory 2023-09-12T11:01:50,553 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:01:50,554 #include "..." search starts here: 2023-09-12T11:01:50,554 #include <...> search starts here: 2023-09-12T11:01:50,555 /usr/include/eigen3 2023-09-12T11:01:50,555 include 2023-09-12T11:01:50,556 /usr/include/python3.11 2023-09-12T11:01:50,556 /usr/include/c++/12 2023-09-12T11:01:50,556 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:01:50,557 /usr/include/c++/12/backward 2023-09-12T11:01:50,557 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:01:50,558 /usr/local/include 2023-09-12T11:01:50,558 /usr/include/arm-linux-gnueabihf 2023-09-12T11:01:50,559 /usr/include 2023-09-12T11:01:50,559 End of search list. 2023-09-12T11:01:50,560 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:01:50,560 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:01:50,561 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:01:50,562 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:01:50,566 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:01:52,136 In file included from include/openbabel/atom.h:33, 2023-09-12T11:01:52,136 from include/openbabel/mol.h:43, 2023-09-12T11:01:52,137 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:01:52,138 from ./src/formats/gamessformat.cpp:19: 2023-09-12T11:01:52,139 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:01:52,139 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:01:52,140 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:01:52,140 | ^ 2023-09-12T11:01:52,141 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:01:52,142 37 | # define UNUSED(x) x 2023-09-12T11:01:52,142 | ^ 2023-09-12T11:01:52,902 In file included from include/openbabel/mol.h:52: 2023-09-12T11:01:52,903 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:52,904 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:52,904 862 | {return new OBVibrationData(*this);} 2023-09-12T11:01:52,905 | ^ 2023-09-12T11:01:52,906 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:01:52,907 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:01:52,907 | ^~~~~~~~ 2023-09-12T11:01:52,908 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:52,909 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:52,910 907 | {return new OBDOSData(*this);} 2023-09-12T11:01:52,910 | ^ 2023-09-12T11:01:52,911 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:01:52,912 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:01:52,913 | ^~~~~~~~ 2023-09-12T11:01:52,927 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:52,927 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:52,928 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:01:52,928 | ^ 2023-09-12T11:01:52,929 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:01:52,930 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:01:52,930 | ^~~~~~~~ 2023-09-12T11:01:52,933 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:01:52,934 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:01:52,934 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:01:52,935 | ^ 2023-09-12T11:01:52,935 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:01:52,936 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:01:52,937 | ^~~~~~~~ 2023-09-12T11:01:53,105 In file included from include/openbabel/format.h:22, 2023-09-12T11:01:53,106 from include/openbabel/obconversion.h:37, 2023-09-12T11:01:53,107 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:01:53,108 include/openbabel/plugin.h: At global scope: 2023-09-12T11:01:53,108 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:01:53,109 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:01:53,110 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:53,111 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:01:53,111 from /usr/include/c++/12/vector:66, 2023-09-12T11:01:53,112 from include/openbabel/mol.h:35: 2023-09-12T11:01:53,113 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:01:53,113 131 | struct binary_function 2023-09-12T11:01:53,114 | ^~~~~~~~~~~~~~~ 2023-09-12T11:01:53,378 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:01:53,379 ./src/formats/gamessformat.cpp:227:9: warning: variable ‘ndummyatoms’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:01:53,380 227 | int ndummyatoms = 0; 2023-09-12T11:01:53,381 | ^~~~~~~~~~~ 2023-09-12T11:01:53,399 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:01:53,400 ./src/formats/gamessformat.cpp:995:14: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 2023-09-12T11:01:53,401 995 | static const bool cmpfn(const char& a, const char& b) { 2023-09-12T11:01:53,401 | ^~~~~ 2023-09-12T11:01:58,467 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:01:58,468 /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]’: 2023-09-12T11:01:58,468 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:01:58,469 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:01:58,469 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:01:58,619 /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]’: 2023-09-12T11:01:58,620 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:01:58,679 /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]’: 2023-09-12T11:01:58,680 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:02,589 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:02,590 ./src/formats/gamessformat.cpp:520:58: warning: ‘lowFreqModesEnd’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:02,591 520 | if (numIntens < lowFreqModesBegin || numIntens > lowFreqModesEnd) 2023-09-12T11:02:02,591 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,592 ./src/formats/gamessformat.cpp:239:9: note: ‘lowFreqModesEnd’ was declared here 2023-09-12T11:02:02,593 239 | int lowFreqModesEnd; // the number of the last low frequency mode 2023-09-12T11:02:02,593 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:02,594 ./src/formats/gamessformat.cpp:520:25: warning: ‘lowFreqModesBegin’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:02,595 520 | if (numIntens < lowFreqModesBegin || numIntens > lowFreqModesEnd) 2023-09-12T11:02:02,596 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,596 ./src/formats/gamessformat.cpp:238:9: note: ‘lowFreqModesBegin’ was declared here 2023-09-12T11:02:02,597 238 | int lowFreqModesBegin; // the number of the first low frequency mode 2023-09-12T11:02:02,598 | ^~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,684 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:02:02,685 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,686 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:279:31: 2023-09-12T11:02:02,686 /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 2023-09-12T11:02:02,687 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,688 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,688 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,689 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:280:31: 2023-09-12T11:02:02,690 /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 2023-09-12T11:02:02,691 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,691 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,692 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,692 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:281:31: 2023-09-12T11:02:02,693 /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 2023-09-12T11:02:02,693 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,694 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,695 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,695 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:302:32: 2023-09-12T11:02:02,696 /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 2023-09-12T11:02:02,696 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,697 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,698 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,698 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:324:34: 2023-09-12T11:02:02,699 /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 2023-09-12T11:02:02,700 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,700 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,701 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,702 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:325:34: 2023-09-12T11:02:02,703 /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 2023-09-12T11:02:02,703 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,704 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,705 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,705 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:326:34: 2023-09-12T11:02:02,706 /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 2023-09-12T11:02:02,707 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,708 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,708 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,709 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:332:34: 2023-09-12T11:02:02,710 /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 2023-09-12T11:02:02,710 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,711 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,711 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,712 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:333:34: 2023-09-12T11:02:02,713 /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 2023-09-12T11:02:02,713 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,714 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,714 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,715 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:334:34: 2023-09-12T11:02:02,715 /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 2023-09-12T11:02:02,716 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,717 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,717 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,718 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:363:32: 2023-09-12T11:02:02,719 /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 2023-09-12T11:02:02,720 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,720 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,721 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,722 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:364:32: 2023-09-12T11:02:02,722 /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 2023-09-12T11:02:02,723 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,724 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,724 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,725 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:365:32: 2023-09-12T11:02:02,726 /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 2023-09-12T11:02:02,726 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,728 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,728 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,729 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:400:36: 2023-09-12T11:02:02,729 /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 2023-09-12T11:02:02,730 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,730 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,731 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,732 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:401:36: 2023-09-12T11:02:02,732 /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 2023-09-12T11:02:02,733 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,733 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,734 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,734 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:402:36: 2023-09-12T11:02:02,735 /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 2023-09-12T11:02:02,736 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:02,736 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:02,737 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,738 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, 2023-09-12T11:02:02,739 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:429:35: 2023-09-12T11:02:02,739 /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 2023-09-12T11:02:02,740 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,741 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,741 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,742 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, 2023-09-12T11:02:02,743 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:511:34: 2023-09-12T11:02:02,744 /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 2023-09-12T11:02:02,744 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,745 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,746 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,746 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, 2023-09-12T11:02:02,747 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:513:34: 2023-09-12T11:02:02,747 /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 2023-09-12T11:02:02,748 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,748 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,749 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,750 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, 2023-09-12T11:02:02,750 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:521:34: 2023-09-12T11:02:02,751 /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 2023-09-12T11:02:02,752 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,752 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,753 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,754 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, 2023-09-12T11:02:02,754 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:528:42: 2023-09-12T11:02:02,755 /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 2023-09-12T11:02:02,756 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,756 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,757 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,758 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, 2023-09-12T11:02:02,758 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:555:24: 2023-09-12T11:02:02,759 /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 2023-09-12T11:02:02,760 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,760 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,761 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,762 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, 2023-09-12T11:02:02,762 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:561:24: 2023-09-12T11:02:02,763 /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 2023-09-12T11:02:02,763 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,764 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,764 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,765 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, 2023-09-12T11:02:02,765 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:568:24: 2023-09-12T11:02:02,766 /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 2023-09-12T11:02:02,767 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,768 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,768 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:02,769 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, 2023-09-12T11:02:02,770 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:576:51: 2023-09-12T11:02:02,771 /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 2023-09-12T11:02:02,772 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,773 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:02,773 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:02,774 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, 2023-09-12T11:02:02,775 inlined from ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gamessformat.cpp:602:31: 2023-09-12T11:02:02,776 /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 2023-09-12T11:02:02,776 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:02,777 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:07,734 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:02:07,735 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/ccrla0GF.s 2023-09-12T11:02:07,739 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:08,704 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/ 2023-09-12T11:02:08,705 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/ 2023-09-12T11:02:08,705 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/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.' 2023-09-12T11:02:08,709 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 2023-09-12T11:02:08,713 Using built-in specs. 2023-09-12T11:02:08,714 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:08,715 Target: arm-linux-gnueabihf 2023-09-12T11:02:08,715 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 2023-09-12T11:02:08,716 Thread model: posix 2023-09-12T11:02:08,717 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:08,718 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:08,718 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:02:08,721 /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/ccNkePQN.s 2023-09-12T11:02:08,727 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:08,727 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:08,728 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:08,729 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:08,729 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:08,730 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:08,730 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:08,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:08,731 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:08,732 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:08,733 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:08,733 #include "..." search starts here: 2023-09-12T11:02:08,734 #include <...> search starts here: 2023-09-12T11:02:08,734 /usr/include/eigen3 2023-09-12T11:02:08,735 include 2023-09-12T11:02:08,736 /usr/include/python3.11 2023-09-12T11:02:08,736 /usr/include/c++/12 2023-09-12T11:02:08,737 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:08,738 /usr/include/c++/12/backward 2023-09-12T11:02:08,738 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:08,739 /usr/local/include 2023-09-12T11:02:08,740 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:08,740 /usr/include 2023-09-12T11:02:08,741 End of search list. 2023-09-12T11:02:08,742 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:08,742 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:08,743 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:08,744 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:08,747 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:10,353 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:10,354 from include/openbabel/mol.h:43, 2023-09-12T11:02:10,354 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:10,355 from ./src/formats/gamessukformat.cpp:14: 2023-09-12T11:02:10,356 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:10,357 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:10,358 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:10,359 | ^ 2023-09-12T11:02:10,361 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:10,361 37 | # define UNUSED(x) x 2023-09-12T11:02:10,362 | ^ 2023-09-12T11:02:11,122 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:11,122 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:11,123 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:11,123 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:11,124 | ^ 2023-09-12T11:02:11,125 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:11,125 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:11,126 | ^~~~~~~~ 2023-09-12T11:02:11,127 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:11,128 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:11,128 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:11,129 | ^ 2023-09-12T11:02:11,130 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:11,131 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:11,131 | ^~~~~~~~ 2023-09-12T11:02:11,146 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:11,147 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:11,148 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:11,149 | ^ 2023-09-12T11:02:11,149 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:11,150 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:11,151 | ^~~~~~~~ 2023-09-12T11:02:11,153 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:11,154 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:11,154 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:11,155 | ^ 2023-09-12T11:02:11,156 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:11,156 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:11,157 | ^~~~~~~~ 2023-09-12T11:02:11,326 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:11,327 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:11,327 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:11,328 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:11,328 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:11,329 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:11,329 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:11,330 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:02:11,330 from /usr/include/c++/12/vector:66, 2023-09-12T11:02:11,331 from include/openbabel/mol.h:35: 2023-09-12T11:02:11,331 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:11,332 131 | struct binary_function 2023-09-12T11:02:11,332 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:11,590 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’: 2023-09-12T11:02:11,591 ./src/formats/gamessukformat.cpp:307:97: warning: unused parameter ‘factor’ [-Wunused-parameter] 2023-09-12T11:02:11,591 307 | bool GAMESSUKFormat::ReadLineZmatrix(OBMol &mol, OBAtom *atom, vector &tokens, double factor, int *zmatLineCount) 2023-09-12T11:02:11,592 | ~~~~~~~^~~~~~ 2023-09-12T11:02:11,638 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadInitialCartesian(OpenBabel::OBMol&, std::istream&)’: 2023-09-12T11:02:11,639 ./src/formats/gamessukformat.cpp:779:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:02:11,639 779 | bool ok=false; 2023-09-12T11:02:11,640 | ^~ 2023-09-12T11:02:11,642 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz1(OpenBabel::OBMol&, std::istream&)’: 2023-09-12T11:02:11,643 ./src/formats/gamessukformat.cpp:845:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:02:11,643 845 | bool ok=false; 2023-09-12T11:02:11,644 | ^~ 2023-09-12T11:02:11,646 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz2(OpenBabel::OBMol&, std::istream&)’: 2023-09-12T11:02:11,647 ./src/formats/gamessukformat.cpp:892:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:02:11,647 892 | bool ok=false; 2023-09-12T11:02:11,648 | ^~ 2023-09-12T11:02:11,679 ./src/formats/gamessukformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSUKOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:11,680 ./src/formats/gamessukformat.cpp:1207:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:02:11,681 1207 | bool ok; 2023-09-12T11:02:11,681 | ^~ 2023-09-12T11:02:18,303 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:02:18,304 /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]’: 2023-09-12T11:02:18,305 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:18,306 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:18,307 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:18,525 /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]’: 2023-09-12T11:02:18,526 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:18,587 /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]’: 2023-09-12T11:02:18,587 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:19,357 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:19,358 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, 2023-09-12T11:02:19,358 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesHessian(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:955:30: 2023-09-12T11:02:19,359 /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 2023-09-12T11:02:19,359 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:19,360 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:19,362 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:02:19,363 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:19,363 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesHessian(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:976:36: 2023-09-12T11:02:19,364 /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 2023-09-12T11:02:19,365 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:19,365 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:19,366 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:19,367 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, 2023-09-12T11:02:19,368 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesHessian(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:977:36: 2023-09-12T11:02:19,368 /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 2023-09-12T11:02:19,369 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:19,369 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:20,323 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:20,324 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, 2023-09-12T11:02:20,324 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesForce(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:1075:30: 2023-09-12T11:02:20,325 /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 2023-09-12T11:02:20,326 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:20,326 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:20,327 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:20,328 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesForce(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:1099:36: 2023-09-12T11:02:20,328 /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 2023-09-12T11:02:20,329 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:20,330 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:20,330 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:20,331 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, 2023-09-12T11:02:20,331 inlined from ‘bool OpenBabel::GAMESSUKOutputFormat::ReadNormalModesForce(OpenBabel::OBMol&, std::istream&)’ at ./src/formats/gamessukformat.cpp:1100:36: 2023-09-12T11:02:20,332 /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 2023-09-12T11:02:20,333 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:20,333 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,092 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:02:21,093 from include/openbabel/mol.h:37: 2023-09-12T11:02:21,094 /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> >]’: 2023-09-12T11:02:21,095 /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 2023-09-12T11:02:21,095 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:02:21,096 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,203 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:02:21,204 /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> >]’: 2023-09-12T11:02:21,205 /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 2023-09-12T11:02:21,206 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:02:21,206 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,206 512 | std::tuple(__k), 2023-09-12T11:02:21,207 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,207 513 | std::tuple<>()); 2023-09-12T11:02:21,208 | ~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,339 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> >]’, 2023-09-12T11:02:21,340 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadVariables(std::istream&, double, std::string)’ at ./src/formats/gamessukformat.cpp:472:26: 2023-09-12T11:02:21,341 /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 2023-09-12T11:02:21,341 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:02:21,342 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,343 512 | std::tuple(__k), 2023-09-12T11:02:21,344 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,344 513 | std::tuple<>()); 2023-09-12T11:02:21,345 | ~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,749 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> >]’, 2023-09-12T11:02:21,750 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:280:32: 2023-09-12T11:02:21,750 /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 2023-09-12T11:02:21,751 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:02:21,752 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,753 512 | std::tuple(__k), 2023-09-12T11:02:21,753 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,754 513 | std::tuple<>()); 2023-09-12T11:02:21,754 | ~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,755 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> >]’, 2023-09-12T11:02:21,756 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:288:32: 2023-09-12T11:02:21,756 /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 2023-09-12T11:02:21,757 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:02:21,757 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,758 512 | std::tuple(__k), 2023-09-12T11:02:21,759 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,760 513 | std::tuple<>()); 2023-09-12T11:02:21,760 | ~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,761 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> >]’, 2023-09-12T11:02:21,762 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:296:32: 2023-09-12T11:02:21,763 /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 2023-09-12T11:02:21,764 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:02:21,764 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,765 512 | std::tuple(__k), 2023-09-12T11:02:21,766 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:21,766 513 | std::tuple<>()); 2023-09-12T11:02:21,767 | ~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,243 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> >]’, 2023-09-12T11:02:22,244 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:386:36: 2023-09-12T11:02:22,244 /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 2023-09-12T11:02:22,245 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:02:22,245 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,246 512 | std::tuple(__k), 2023-09-12T11:02:22,246 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:22,247 513 | std::tuple<>()); 2023-09-12T11:02:22,247 | ~~~~~~~~~~~~~~~ 2023-09-12T11:02:24,055 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/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/' 2023-09-12T11:02:24,056 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/ccNkePQN.s 2023-09-12T11:02:24,061 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:25,121 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/ 2023-09-12T11:02:25,122 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/ 2023-09-12T11:02:25,122 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:02:25,126 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 2023-09-12T11:02:25,131 Using built-in specs. 2023-09-12T11:02:25,132 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:25,132 Target: arm-linux-gnueabihf 2023-09-12T11:02:25,132 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 2023-09-12T11:02:25,133 Thread model: posix 2023-09-12T11:02:25,133 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:25,134 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:25,134 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:02:25,135 /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/ccRDROUY.s 2023-09-12T11:02:25,143 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:25,144 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:25,145 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:25,146 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:25,146 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:25,147 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:25,147 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:25,148 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:25,148 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:25,149 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:25,150 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:25,150 #include "..." search starts here: 2023-09-12T11:02:25,151 #include <...> search starts here: 2023-09-12T11:02:25,151 /usr/include/eigen3 2023-09-12T11:02:25,152 include 2023-09-12T11:02:25,153 /usr/include/python3.11 2023-09-12T11:02:25,153 /usr/include/c++/12 2023-09-12T11:02:25,154 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:25,154 /usr/include/c++/12/backward 2023-09-12T11:02:25,154 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:25,155 /usr/local/include 2023-09-12T11:02:25,155 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:25,156 /usr/include 2023-09-12T11:02:25,156 End of search list. 2023-09-12T11:02:25,157 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:25,157 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:25,158 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:25,158 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:25,161 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:26,747 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:26,748 from include/openbabel/mol.h:43, 2023-09-12T11:02:26,748 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:02:26,749 from ./src/formats/gausscubeformat.cpp:28: 2023-09-12T11:02:26,749 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:26,750 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:26,750 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:26,751 | ^ 2023-09-12T11:02:26,751 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:26,752 37 | # define UNUSED(x) x 2023-09-12T11:02:26,753 | ^ 2023-09-12T11:02:27,514 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:27,515 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:27,516 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:27,516 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:27,517 | ^ 2023-09-12T11:02:27,518 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:27,519 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:27,520 | ^~~~~~~~ 2023-09-12T11:02:27,520 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:27,521 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:27,522 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:27,522 | ^ 2023-09-12T11:02:27,523 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:27,524 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:27,524 | ^~~~~~~~ 2023-09-12T11:02:27,538 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:27,539 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:27,540 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:27,541 | ^ 2023-09-12T11:02:27,541 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:27,542 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:27,542 | ^~~~~~~~ 2023-09-12T11:02:27,545 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:27,545 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:27,546 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:27,546 | ^ 2023-09-12T11:02:27,547 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:27,548 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:27,548 | ^~~~~~~~ 2023-09-12T11:02:27,717 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:27,718 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:27,719 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:02:27,719 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:27,720 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:27,720 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:27,721 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:27,722 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:02:27,723 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:02:27,723 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:02:27,724 from /usr/include/c++/12/ios:42, 2023-09-12T11:02:27,725 from /usr/include/c++/12/istream:38, 2023-09-12T11:02:27,725 from /usr/include/c++/12/sstream:38, 2023-09-12T11:02:27,726 from ./src/formats/gausscubeformat.cpp:25: 2023-09-12T11:02:27,727 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:27,727 131 | struct binary_function 2023-09-12T11:02:27,728 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:27,919 ./src/formats/gausscubeformat.cpp: In member function ‘virtual int OpenBabel::OBGaussianCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:02:27,920 ./src/formats/gausscubeformat.cpp:79:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:02:27,921 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:02:27,921 | ~~~~^ 2023-09-12T11:02:27,922 ./src/formats/gausscubeformat.cpp:79:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:02:27,923 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:02:27,924 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:02:28,002 ./src/formats/gausscubeformat.cpp: In member function ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:28,003 ./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] 2023-09-12T11:02:28,003 425 | while (vgd.size() < nCubes) 2023-09-12T11:02:28,004 | ~~~~~~~~~~~^~~~~~~~ 2023-09-12T11:02:28,012 ./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] 2023-09-12T11:02:28,013 472 | while (values.size() < n*nCubes) 2023-09-12T11:02:28,014 | ~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:02:28,035 ./src/formats/gausscubeformat.cpp:107:17: warning: unused variable ‘title’ [-Wunused-variable] 2023-09-12T11:02:28,036 107 | const char* title = pConv->GetTitle(); 2023-09-12T11:02:28,036 | ^~~~~ 2023-09-12T11:02:31,830 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:02:31,830 from include/openbabel/mol.h:35: 2023-09-12T11:02:31,831 /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]’: 2023-09-12T11:02:31,832 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:31,836 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:31,839 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:31,931 /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]’: 2023-09-12T11:02:31,932 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:33,376 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:33,377 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, 2023-09-12T11:02:33,378 inlined from ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gausscubeformat.cpp:500:25: 2023-09-12T11:02:33,378 /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 2023-09-12T11:02:33,379 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:33,380 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:33,380 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:02:33,381 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:33,382 inlined from ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gausscubeformat.cpp:511:25: 2023-09-12T11:02:33,382 /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 2023-09-12T11:02:33,383 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:33,384 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:36,621 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:02:36,622 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/ccRDROUY.s 2023-09-12T11:02:36,627 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:37,212 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/ 2023-09-12T11:02:37,213 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/ 2023-09-12T11:02:37,213 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:02:37,215 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 2023-09-12T11:02:37,220 Using built-in specs. 2023-09-12T11:02:37,220 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:37,221 Target: arm-linux-gnueabihf 2023-09-12T11:02:37,222 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 2023-09-12T11:02:37,222 Thread model: posix 2023-09-12T11:02:37,223 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:37,223 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:37,224 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:02:37,225 /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/ccxI9vWw.s 2023-09-12T11:02:37,233 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:37,234 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:37,235 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:37,235 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:37,236 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:37,236 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:37,237 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:37,238 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:37,238 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:37,239 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:37,240 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:37,240 #include "..." search starts here: 2023-09-12T11:02:37,241 #include <...> search starts here: 2023-09-12T11:02:37,242 /usr/include/eigen3 2023-09-12T11:02:37,242 include 2023-09-12T11:02:37,243 /usr/include/python3.11 2023-09-12T11:02:37,244 /usr/include/c++/12 2023-09-12T11:02:37,244 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:37,245 /usr/include/c++/12/backward 2023-09-12T11:02:37,246 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:37,246 /usr/local/include 2023-09-12T11:02:37,247 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:37,248 /usr/include 2023-09-12T11:02:37,248 End of search list. 2023-09-12T11:02:37,249 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:37,249 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:37,250 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:37,251 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:37,252 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:02:38,898 In file included from include/openbabel/atom.h:33, 2023-09-12T11:02:38,899 from include/openbabel/mol.h:43, 2023-09-12T11:02:38,900 from include/openbabel/data_utilities.h:25, 2023-09-12T11:02:38,900 from ./src/formats/gaussformat.cpp:18: 2023-09-12T11:02:38,901 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:02:38,902 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:02:38,903 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:02:38,904 | ^ 2023-09-12T11:02:38,904 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:02:38,905 37 | # define UNUSED(x) x 2023-09-12T11:02:38,905 | ^ 2023-09-12T11:02:39,571 In file included from include/openbabel/mol.h:52: 2023-09-12T11:02:39,571 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:39,572 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:39,572 862 | {return new OBVibrationData(*this);} 2023-09-12T11:02:39,573 | ^ 2023-09-12T11:02:39,574 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:02:39,574 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:02:39,575 | ^~~~~~~~ 2023-09-12T11:02:39,576 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:39,576 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:39,577 907 | {return new OBDOSData(*this);} 2023-09-12T11:02:39,578 | ^ 2023-09-12T11:02:39,578 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:02:39,579 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:02:39,580 | ^~~~~~~~ 2023-09-12T11:02:39,595 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:39,596 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:39,596 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:02:39,597 | ^ 2023-09-12T11:02:39,598 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:02:39,599 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:02:39,599 | ^~~~~~~~ 2023-09-12T11:02:39,601 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:02:39,602 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:02:39,602 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:02:39,603 | ^ 2023-09-12T11:02:39,604 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:02:39,605 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:02:39,606 | ^~~~~~~~ 2023-09-12T11:02:39,774 In file included from include/openbabel/format.h:22, 2023-09-12T11:02:39,774 from include/openbabel/obconversion.h:37, 2023-09-12T11:02:39,775 from include/openbabel/obmolecformat.h:31, 2023-09-12T11:02:39,776 from ./src/formats/gaussformat.cpp:19: 2023-09-12T11:02:39,776 include/openbabel/plugin.h: At global scope: 2023-09-12T11:02:39,777 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:02:39,777 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:02:39,778 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:39,778 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:02:39,779 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:02:39,780 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:02:39,780 from /usr/include/c++/12/ios:42, 2023-09-12T11:02:39,781 from /usr/include/c++/12/istream:38, 2023-09-12T11:02:39,781 from /usr/include/c++/12/fstream:38, 2023-09-12T11:02:39,782 from include/openbabel/data.h:27, 2023-09-12T11:02:39,782 from ./src/formats/gaussformat.cpp:17: 2023-09-12T11:02:39,783 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:02:39,784 131 | struct binary_function 2023-09-12T11:02:39,784 | ^~~~~~~~~~~~~~~ 2023-09-12T11:02:40,015 ./src/formats/gaussformat.cpp: In function ‘void OpenBabel::add_unique_pairdata_to_mol(OBMol*, std::string, std::string, int)’: 2023-09-12T11:02:40,015 ./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] 2023-09-12T11:02:40,016 275 | if (vs.size() >= start) 2023-09-12T11:02:40,017 | ~~~~~~~~~~^~~~~~~~ 2023-09-12T11:02:40,018 ./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] 2023-09-12T11:02:40,019 278 | for(i=start+1; (i)’: 2023-09-12T11:02:40,025 ./src/formats/gaussformat.cpp:332:17: warning: unused variable ‘pg’ [-Wunused-variable] 2023-09-12T11:02:40,026 332 | const char *pg = obPG.IdentifyPointGroup(); 2023-09-12T11:02:40,027 | ^~ 2023-09-12T11:02:46,743 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:02:46,744 from include/openbabel/data.h:28: 2023-09-12T11:02:46,744 /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]’: 2023-09-12T11:02:46,745 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:46,746 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:46,746 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:46,779 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:02:46,780 /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]’: 2023-09-12T11:02:46,781 /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 2023-09-12T11:02:46,782 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:46,783 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:46,956 /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]’: 2023-09-12T11:02:46,956 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:46,957 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:46,957 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:46,991 /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]’: 2023-09-12T11:02:46,992 /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 2023-09-12T11:02:46,992 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:46,993 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:47,026 /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]’: 2023-09-12T11:02:47,026 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:02:47,027 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:02:47,028 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,819 ./src/formats/gaussformat.cpp: In member function ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:02:50,820 ./src/formats/gaussformat.cpp:1164:25: warning: ‘CV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:50,820 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:02:50,821 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,822 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:02:50,823 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,823 ./src/formats/gaussformat.cpp:450:32: note: ‘CV’ was declared here 2023-09-12T11:02:50,824 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:02:50,825 | ^~ 2023-09-12T11:02:50,825 ./src/formats/gaussformat.cpp:1164:25: warning: ‘E0’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:50,826 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:02:50,827 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,828 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:02:50,828 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,829 ./src/formats/gaussformat.cpp:450:29: note: ‘E0’ was declared here 2023-09-12T11:02:50,830 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:02:50,830 | ^~ 2023-09-12T11:02:50,831 ./src/formats/gaussformat.cpp:1164:25: warning: ‘Gcorr’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:50,832 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:02:50,832 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,834 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:02:50,834 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,835 ./src/formats/gaussformat.cpp:450:23: note: ‘Gcorr’ was declared here 2023-09-12T11:02:50,836 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:02:50,836 | ^~~~~ 2023-09-12T11:02:50,837 ./src/formats/gaussformat.cpp:1164:25: warning: ‘Hcorr’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:50,837 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:02:50,838 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,838 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:02:50,839 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,840 ./src/formats/gaussformat.cpp:450:17: note: ‘Hcorr’ was declared here 2023-09-12T11:02:50,840 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:02:50,841 | ^~~~~ 2023-09-12T11:02:50,842 ./src/formats/gaussformat.cpp:1164:25: warning: ‘ezpe’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:02:50,842 1164 | extract_thermo(&mol,thermo_method,temperature,ezpe, 2023-09-12T11:02:50,843 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,843 1165 | Hcorr,Gcorr,E0,CV,RotSymNum,Scomponents); 2023-09-12T11:02:50,844 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,844 ./src/formats/gaussformat.cpp:450:12: note: ‘ezpe’ was declared here 2023-09-12T11:02:50,845 450 | double ezpe,Hcorr,Gcorr,E0,CV; 2023-09-12T11:02:50,846 | ^~~~ 2023-09-12T11:02:50,939 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,940 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:609:42: 2023-09-12T11:02:50,940 /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 2023-09-12T11:02:50,941 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:50,942 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:50,943 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,944 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:610:42: 2023-09-12T11:02:50,944 /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 2023-09-12T11:02:50,945 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:50,946 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:50,946 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,947 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:611:42: 2023-09-12T11:02:50,948 /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 2023-09-12T11:02:50,948 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:50,949 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:50,958 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,959 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, 2023-09-12T11:02:50,960 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:841:34: 2023-09-12T11:02:50,960 /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 2023-09-12T11:02:50,961 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:50,961 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,962 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,962 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, 2023-09-12T11:02:50,963 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:847:34: 2023-09-12T11:02:50,964 /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 2023-09-12T11:02:50,964 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:50,965 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,965 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:50,966 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, 2023-09-12T11:02:50,966 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:866:31: 2023-09-12T11:02:50,967 /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 2023-09-12T11:02:50,968 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:50,969 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,969 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:50,970 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, 2023-09-12T11:02:50,971 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:868:31: 2023-09-12T11:02:50,971 /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 2023-09-12T11:02:50,972 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:50,973 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,974 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:02:50,974 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, 2023-09-12T11:02:50,975 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:870:31: 2023-09-12T11:02:50,975 /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 2023-09-12T11:02:50,976 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:50,976 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,977 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,977 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, 2023-09-12T11:02:50,978 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:904:32: 2023-09-12T11:02:50,978 /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 2023-09-12T11:02:50,979 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:50,980 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,981 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,981 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, 2023-09-12T11:02:50,982 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:964:33: 2023-09-12T11:02:50,983 /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 2023-09-12T11:02:50,984 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:02:50,984 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:02:50,989 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:02:50,990 inlined from ‘virtual bool OpenBabel::GaussianOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/gaussformat.cpp:1187:39: 2023-09-12T11:02:50,990 /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 2023-09-12T11:02:50,991 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:02:50,992 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:02:57,292 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:02:57,293 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/ccxI9vWw.s 2023-09-12T11:02:57,300 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:02:58,470 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/ 2023-09-12T11:02:58,470 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/ 2023-09-12T11:02:58,471 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:02:58,475 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 2023-09-12T11:02:58,480 Using built-in specs. 2023-09-12T11:02:58,481 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:02:58,481 Target: arm-linux-gnueabihf 2023-09-12T11:02:58,482 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 2023-09-12T11:02:58,483 Thread model: posix 2023-09-12T11:02:58,483 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:02:58,484 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:02:58,484 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:02:58,485 /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/ccTc7J1Y.s 2023-09-12T11:02:58,494 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:58,495 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:58,496 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:58,496 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:58,497 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:02:58,497 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:02:58,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:02:58,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:02:58,499 ignoring duplicate directory "/usr/include/" 2023-09-12T11:02:58,500 as it is a non-system directory that duplicates a system directory 2023-09-12T11:02:58,501 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:02:58,501 #include "..." search starts here: 2023-09-12T11:02:58,502 #include <...> search starts here: 2023-09-12T11:02:58,503 /usr/include/eigen3 2023-09-12T11:02:58,503 include 2023-09-12T11:02:58,504 /usr/include/python3.11 2023-09-12T11:02:58,505 /usr/include/c++/12 2023-09-12T11:02:58,505 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:02:58,506 /usr/include/c++/12/backward 2023-09-12T11:02:58,507 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:02:58,507 /usr/local/include 2023-09-12T11:02:58,508 /usr/include/arm-linux-gnueabihf 2023-09-12T11:02:58,509 /usr/include 2023-09-12T11:02:58,509 End of search list. 2023-09-12T11:02:58,510 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:02:58,511 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:02:58,512 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:02:58,513 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:02:58,513 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:00,074 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:00,075 from include/openbabel/mol.h:43, 2023-09-12T11:03:00,075 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:00,076 from ./src/formats/gausszmatformat.cpp:16: 2023-09-12T11:03:00,077 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:00,077 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:00,078 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:00,079 | ^ 2023-09-12T11:03:00,080 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:00,080 37 | # define UNUSED(x) x 2023-09-12T11:03:00,081 | ^ 2023-09-12T11:03:00,841 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:00,842 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:00,842 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:00,843 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:00,844 | ^ 2023-09-12T11:03:00,844 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:00,845 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:00,845 | ^~~~~~~~ 2023-09-12T11:03:00,846 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:00,847 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:00,848 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:00,848 | ^ 2023-09-12T11:03:00,849 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:00,850 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:00,850 | ^~~~~~~~ 2023-09-12T11:03:00,865 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:00,866 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:00,867 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:00,868 | ^ 2023-09-12T11:03:00,869 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:00,869 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:00,870 | ^~~~~~~~ 2023-09-12T11:03:00,872 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:00,872 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:00,873 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:00,874 | ^ 2023-09-12T11:03:00,875 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:00,875 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:00,876 | ^~~~~~~~ 2023-09-12T11:03:01,045 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:01,045 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:01,046 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:01,047 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:01,047 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:01,048 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:01,049 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:01,049 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:01,050 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:01,050 from include/openbabel/mol.h:35: 2023-09-12T11:03:01,051 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:01,051 131 | struct binary_function 2023-09-12T11:03:01,052 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:04,797 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:03:04,798 from include/openbabel/mol.h:37: 2023-09-12T11:03:04,799 /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> >]’: 2023-09-12T11:03:04,799 /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 2023-09-12T11:03:04,800 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:03:04,801 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:06,460 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:06,461 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/ccTc7J1Y.s 2023-09-12T11:03:06,465 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:06,846 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/ 2023-09-12T11:03:06,846 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/ 2023-09-12T11:03:06,847 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/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.' 2023-09-12T11:03:06,848 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 2023-09-12T11:03:06,853 Using built-in specs. 2023-09-12T11:03:06,854 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:06,854 Target: arm-linux-gnueabihf 2023-09-12T11:03:06,854 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 2023-09-12T11:03:06,855 Thread model: posix 2023-09-12T11:03:06,856 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:06,856 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:06,857 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:06,858 /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/cc4I2BSj.s 2023-09-12T11:03:06,866 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:06,866 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:06,868 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:06,868 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:06,869 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:06,870 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:06,871 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:06,871 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:06,872 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:06,872 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:06,873 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:06,873 #include "..." search starts here: 2023-09-12T11:03:06,873 #include <...> search starts here: 2023-09-12T11:03:06,874 /usr/include/eigen3 2023-09-12T11:03:06,874 include 2023-09-12T11:03:06,875 /usr/include/python3.11 2023-09-12T11:03:06,875 /usr/include/c++/12 2023-09-12T11:03:06,876 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:06,876 /usr/include/c++/12/backward 2023-09-12T11:03:06,876 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:06,877 /usr/local/include 2023-09-12T11:03:06,877 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:06,878 /usr/include 2023-09-12T11:03:06,878 End of search list. 2023-09-12T11:03:06,879 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:06,879 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:06,880 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:06,881 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:06,885 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:08,445 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:08,446 from include/openbabel/mol.h:43, 2023-09-12T11:03:08,446 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:08,447 from ./src/formats/genbankformat.cpp:19: 2023-09-12T11:03:08,448 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:08,449 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:08,449 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:08,450 | ^ 2023-09-12T11:03:08,451 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:08,451 37 | # define UNUSED(x) x 2023-09-12T11:03:08,452 | ^ 2023-09-12T11:03:09,214 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:09,214 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:09,215 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:09,216 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:09,217 | ^ 2023-09-12T11:03:09,217 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:09,218 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:09,219 | ^~~~~~~~ 2023-09-12T11:03:09,220 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:09,220 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:09,221 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:09,222 | ^ 2023-09-12T11:03:09,223 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:09,223 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:09,224 | ^~~~~~~~ 2023-09-12T11:03:09,239 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:09,240 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:09,240 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:09,241 | ^ 2023-09-12T11:03:09,242 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:09,242 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:09,243 | ^~~~~~~~ 2023-09-12T11:03:09,246 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:09,247 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:09,247 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:09,248 | ^ 2023-09-12T11:03:09,248 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:09,249 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:09,250 | ^~~~~~~~ 2023-09-12T11:03:09,418 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:09,419 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:09,420 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:09,420 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:09,421 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:09,422 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:09,422 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:09,423 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:09,424 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:09,424 from include/openbabel/mol.h:35: 2023-09-12T11:03:09,425 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:09,426 131 | struct binary_function 2023-09-12T11:03:09,426 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:11,905 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/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/' 2023-09-12T11:03:11,905 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/cc4I2BSj.s 2023-09-12T11:03:11,910 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:12,049 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/ 2023-09-12T11:03:12,049 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/ 2023-09-12T11:03:12,050 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/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.' 2023-09-12T11:03:12,051 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 2023-09-12T11:03:12,055 Using built-in specs. 2023-09-12T11:03:12,056 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:12,056 Target: arm-linux-gnueabihf 2023-09-12T11:03:12,057 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 2023-09-12T11:03:12,057 Thread model: posix 2023-09-12T11:03:12,058 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:12,059 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:12,059 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/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/' 2023-09-12T11:03:12,060 /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/ccTry3qm.s 2023-09-12T11:03:12,068 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:12,069 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:12,070 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:12,070 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:12,071 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:12,071 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:12,071 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:12,072 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:12,072 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:12,073 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:12,073 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:12,074 #include "..." search starts here: 2023-09-12T11:03:12,074 #include <...> search starts here: 2023-09-12T11:03:12,075 /usr/include/eigen3 2023-09-12T11:03:12,076 include 2023-09-12T11:03:12,076 /usr/include/python3.11 2023-09-12T11:03:12,077 /usr/include/c++/12 2023-09-12T11:03:12,078 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:12,078 /usr/include/c++/12/backward 2023-09-12T11:03:12,079 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:12,079 /usr/local/include 2023-09-12T11:03:12,080 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:12,081 /usr/include 2023-09-12T11:03:12,081 End of search list. 2023-09-12T11:03:12,082 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:12,083 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:12,084 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:12,085 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:12,086 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:13,681 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:13,682 from include/openbabel/mol.h:43, 2023-09-12T11:03:13,683 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:13,683 from ./src/formats/ghemicalformat.cpp:17: 2023-09-12T11:03:13,684 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:13,685 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:13,685 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:13,686 | ^ 2023-09-12T11:03:13,687 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:13,687 37 | # define UNUSED(x) x 2023-09-12T11:03:13,688 | ^ 2023-09-12T11:03:14,449 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:14,450 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:14,450 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:14,451 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:14,451 | ^ 2023-09-12T11:03:14,452 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:14,452 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:14,453 | ^~~~~~~~ 2023-09-12T11:03:14,454 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:14,455 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:14,455 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:14,456 | ^ 2023-09-12T11:03:14,457 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:14,457 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:14,458 | ^~~~~~~~ 2023-09-12T11:03:14,473 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:14,474 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:14,474 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:14,475 | ^ 2023-09-12T11:03:14,476 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:14,477 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:14,477 | ^~~~~~~~ 2023-09-12T11:03:14,479 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:14,480 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:14,481 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:14,481 | ^ 2023-09-12T11:03:14,482 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:14,483 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:14,484 | ^~~~~~~~ 2023-09-12T11:03:14,652 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:14,652 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:14,653 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:14,654 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:14,655 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:14,655 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:14,656 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:14,656 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:14,657 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:14,657 from include/openbabel/mol.h:35: 2023-09-12T11:03:14,658 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:14,659 131 | struct binary_function 2023-09-12T11:03:14,659 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:17,925 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/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/' 2023-09-12T11:03:17,926 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/ccTry3qm.s 2023-09-12T11:03:17,930 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:18,134 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/ 2023-09-12T11:03:18,134 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/ 2023-09-12T11:03:18,135 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:03:18,136 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 2023-09-12T11:03:18,141 Using built-in specs. 2023-09-12T11:03:18,142 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:18,142 Target: arm-linux-gnueabihf 2023-09-12T11:03:18,143 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 2023-09-12T11:03:18,144 Thread model: posix 2023-09-12T11:03:18,144 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:18,145 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:18,145 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:18,146 /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/cchNDQCk.s 2023-09-12T11:03:18,154 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:18,155 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:18,156 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:18,157 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:18,157 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:18,158 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:18,159 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:18,159 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:18,160 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:18,161 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:18,161 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:18,162 #include "..." search starts here: 2023-09-12T11:03:18,162 #include <...> search starts here: 2023-09-12T11:03:18,163 /usr/include/eigen3 2023-09-12T11:03:18,164 include 2023-09-12T11:03:18,164 /usr/include/python3.11 2023-09-12T11:03:18,165 /usr/include/c++/12 2023-09-12T11:03:18,165 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:18,166 /usr/include/c++/12/backward 2023-09-12T11:03:18,167 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:18,167 /usr/local/include 2023-09-12T11:03:18,168 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:18,169 /usr/include 2023-09-12T11:03:18,169 End of search list. 2023-09-12T11:03:18,170 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:18,171 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:18,173 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:18,174 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:18,174 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:19,744 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:19,745 from include/openbabel/mol.h:43, 2023-09-12T11:03:19,745 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:19,746 from ./src/formats/groformat.cpp:16: 2023-09-12T11:03:19,746 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:19,747 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:19,748 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:19,748 | ^ 2023-09-12T11:03:19,749 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:19,749 37 | # define UNUSED(x) x 2023-09-12T11:03:19,750 | ^ 2023-09-12T11:03:20,513 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:20,513 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:20,514 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:20,514 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:20,515 | ^ 2023-09-12T11:03:20,516 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:20,517 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:20,517 | ^~~~~~~~ 2023-09-12T11:03:20,519 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:20,520 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:20,521 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:20,521 | ^ 2023-09-12T11:03:20,522 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:20,523 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:20,524 | ^~~~~~~~ 2023-09-12T11:03:20,539 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:20,540 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:20,541 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:20,541 | ^ 2023-09-12T11:03:20,542 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:20,543 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:20,544 | ^~~~~~~~ 2023-09-12T11:03:20,547 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:20,548 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:20,548 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:20,549 | ^ 2023-09-12T11:03:20,550 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:20,550 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:20,551 | ^~~~~~~~ 2023-09-12T11:03:20,720 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:20,720 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:20,721 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:20,721 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:20,722 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:20,722 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:20,723 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:20,723 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:20,724 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:20,725 from include/openbabel/mol.h:35: 2023-09-12T11:03:20,725 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:20,726 131 | struct binary_function 2023-09-12T11:03:20,727 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:24,750 ./src/formats/groformat.cpp: In member function ‘virtual bool OpenBabel::GROFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:03:24,750 ./src/formats/groformat.cpp:273:19: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:03:24,751 273 | res->AddAtom(atom); 2023-09-12T11:03:24,752 | ~~~~~~~~~~~~^~~~~~ 2023-09-12T11:03:24,752 ./src/formats/groformat.cpp:163:14: note: ‘res’ was declared here 2023-09-12T11:03:24,753 163 | OBResidue* res; 2023-09-12T11:03:24,754 | ^~~ 2023-09-12T11:03:26,354 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:26,355 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/cchNDQCk.s 2023-09-12T11:03:26,359 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:26,732 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/ 2023-09-12T11:03:26,733 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/ 2023-09-12T11:03:26,734 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:03:26,735 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 2023-09-12T11:03:26,739 Using built-in specs. 2023-09-12T11:03:26,740 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:26,740 Target: arm-linux-gnueabihf 2023-09-12T11:03:26,741 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 2023-09-12T11:03:26,741 Thread model: posix 2023-09-12T11:03:26,742 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:26,742 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:26,743 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:26,743 /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/ccbuueMP.s 2023-09-12T11:03:26,752 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:26,753 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:26,754 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:26,755 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:26,755 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:26,756 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:26,756 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:26,756 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:26,757 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:26,757 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:26,758 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:26,758 #include "..." search starts here: 2023-09-12T11:03:26,759 #include <...> search starts here: 2023-09-12T11:03:26,759 /usr/include/eigen3 2023-09-12T11:03:26,760 include 2023-09-12T11:03:26,760 /usr/include/python3.11 2023-09-12T11:03:26,760 /usr/include/c++/12 2023-09-12T11:03:26,761 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:26,761 /usr/include/c++/12/backward 2023-09-12T11:03:26,762 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:26,762 /usr/local/include 2023-09-12T11:03:26,762 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:26,763 /usr/include 2023-09-12T11:03:26,763 End of search list. 2023-09-12T11:03:26,764 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:26,764 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:26,766 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:26,766 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:26,773 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:28,342 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:28,342 from include/openbabel/mol.h:43, 2023-09-12T11:03:28,343 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:28,344 from ./src/formats/gromos96format.cpp:54: 2023-09-12T11:03:28,345 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:28,345 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:28,346 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:28,347 | ^ 2023-09-12T11:03:28,347 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:28,348 37 | # define UNUSED(x) x 2023-09-12T11:03:28,349 | ^ 2023-09-12T11:03:29,112 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:29,112 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,113 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,114 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:29,114 | ^ 2023-09-12T11:03:29,115 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:29,116 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:29,117 | ^~~~~~~~ 2023-09-12T11:03:29,118 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,118 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,119 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:29,119 | ^ 2023-09-12T11:03:29,120 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:29,120 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:29,121 | ^~~~~~~~ 2023-09-12T11:03:29,136 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,137 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,137 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:29,138 | ^ 2023-09-12T11:03:29,138 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:29,139 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:29,140 | ^~~~~~~~ 2023-09-12T11:03:29,142 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:29,143 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:29,144 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:29,145 | ^ 2023-09-12T11:03:29,146 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:29,146 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:29,147 | ^~~~~~~~ 2023-09-12T11:03:29,315 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:29,316 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:29,316 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:29,317 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:29,318 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:29,318 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:29,319 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:29,320 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:29,321 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:29,321 from include/openbabel/mol.h:35: 2023-09-12T11:03:29,322 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:29,323 131 | struct binary_function 2023-09-12T11:03:29,324 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:31,135 ./src/formats/gromos96format.cpp: In member function ‘virtual bool OpenBabel::GROMOS96Format::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:03:31,136 ./src/formats/gromos96format.cpp:140:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2023-09-12T11:03:31,136 140 | strncpy(type_name,etab.GetSymbol(atom->GetAtomicNum()), 16); 2023-09-12T11:03:31,137 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:31,137 ./src/formats/gromos96format.cpp:132:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2023-09-12T11:03:31,138 132 | strncpy(res_name,(char*)res->GetName().c_str(), 16); 2023-09-12T11:03:31,139 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:31,139 ./src/formats/gromos96format.cpp:134:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2023-09-12T11:03:31,140 134 | strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16); 2023-09-12T11:03:31,140 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:31,802 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:31,803 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/ccbuueMP.s 2023-09-12T11:03:31,807 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:31,951 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/ 2023-09-12T11:03:31,951 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/ 2023-09-12T11:03:31,952 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/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.' 2023-09-12T11:03:31,953 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 2023-09-12T11:03:31,957 Using built-in specs. 2023-09-12T11:03:31,957 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:31,958 Target: arm-linux-gnueabihf 2023-09-12T11:03:31,959 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 2023-09-12T11:03:31,959 Thread model: posix 2023-09-12T11:03:31,960 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:31,960 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:31,961 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:31,961 /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/ccwWoi5v.s 2023-09-12T11:03:31,971 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:31,971 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:31,973 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:31,973 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:31,974 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:31,974 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:31,975 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:31,975 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:31,976 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:31,976 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:31,977 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:31,978 #include "..." search starts here: 2023-09-12T11:03:31,978 #include <...> search starts here: 2023-09-12T11:03:31,979 /usr/include/eigen3 2023-09-12T11:03:31,979 include 2023-09-12T11:03:31,980 /usr/include/python3.11 2023-09-12T11:03:31,981 /usr/include/c++/12 2023-09-12T11:03:31,981 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:31,982 /usr/include/c++/12/backward 2023-09-12T11:03:31,983 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:31,984 /usr/local/include 2023-09-12T11:03:31,984 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:31,984 /usr/include 2023-09-12T11:03:31,985 End of search list. 2023-09-12T11:03:31,985 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:31,985 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 2023-09-12T11:03:31,986 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:31,987 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:31,997 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:33,561 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:33,561 from include/openbabel/mol.h:43, 2023-09-12T11:03:33,562 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:33,562 from ./src/formats/gulpformat.cpp:16: 2023-09-12T11:03:33,563 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:33,563 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:33,564 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:33,564 | ^ 2023-09-12T11:03:33,565 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:33,565 37 | # define UNUSED(x) x 2023-09-12T11:03:33,566 | ^ 2023-09-12T11:03:34,331 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:34,332 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:34,332 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:34,333 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:34,334 | ^ 2023-09-12T11:03:34,334 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:34,335 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:34,336 | ^~~~~~~~ 2023-09-12T11:03:34,339 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:34,340 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:34,340 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:34,341 | ^ 2023-09-12T11:03:34,342 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:34,342 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:34,343 | ^~~~~~~~ 2023-09-12T11:03:34,358 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:34,359 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:34,360 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:34,360 | ^ 2023-09-12T11:03:34,361 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:34,362 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:34,363 | ^~~~~~~~ 2023-09-12T11:03:34,364 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:34,365 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:34,366 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:34,366 | ^ 2023-09-12T11:03:34,367 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:34,367 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:34,368 | ^~~~~~~~ 2023-09-12T11:03:34,537 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:34,537 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:34,538 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:34,539 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:34,540 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:34,540 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:34,541 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:34,542 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:34,543 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:34,543 from include/openbabel/mol.h:35: 2023-09-12T11:03:34,544 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:34,545 131 | struct binary_function 2023-09-12T11:03:34,546 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:34,736 ./src/formats/gulpformat.cpp: In member function ‘virtual int OpenBabel::GULPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:03:34,737 ./src/formats/gulpformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:03:34,738 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:03:34,738 | ~~~~^ 2023-09-12T11:03:34,739 ./src/formats/gulpformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:03:34,740 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:03:34,740 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:03:37,505 ./src/formats/gulpformat.cpp: In member function ‘virtual bool OpenBabel::GULPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:03:37,506 ./src/formats/gulpformat.cpp:359:15: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:03:37,507 359 | snprintf(tag, BUFF_SIZE, "%f", pv_eV); 2023-09-12T11:03:37,508 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:37,508 ./src/formats/gulpformat.cpp:88:25: note: ‘pv_eV’ was declared here 2023-09-12T11:03:37,509 88 | double enthalpy_eV, pv_eV; 2023-09-12T11:03:37,510 | ^~~~~ 2023-09-12T11:03:37,511 ./src/formats/gulpformat.cpp:357:15: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:03:37,512 357 | snprintf(tag, BUFF_SIZE, "%f", enthalpy_eV); 2023-09-12T11:03:37,512 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:37,513 ./src/formats/gulpformat.cpp:88:12: note: ‘enthalpy_eV’ was declared here 2023-09-12T11:03:37,514 88 | double enthalpy_eV, pv_eV; 2023-09-12T11:03:37,514 | ^~~~~~~~~~~ 2023-09-12T11:03:38,941 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/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/' 2023-09-12T11:03:38,942 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/gulpformat.o /tmp/ccwWoi5v.s 2023-09-12T11:03:38,946 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:39,218 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/ 2023-09-12T11:03:39,219 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/ 2023-09-12T11:03:39,220 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:03:39,221 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 2023-09-12T11:03:39,225 Using built-in specs. 2023-09-12T11:03:39,226 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:39,227 Target: arm-linux-gnueabihf 2023-09-12T11:03:39,227 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 2023-09-12T11:03:39,228 Thread model: posix 2023-09-12T11:03:39,228 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:39,229 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:39,230 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:39,230 /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/ccHoVToD.s 2023-09-12T11:03:39,238 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:39,239 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:39,240 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:39,241 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:39,241 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:39,242 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:39,243 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:39,243 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:39,244 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:39,245 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:39,245 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:39,246 #include "..." search starts here: 2023-09-12T11:03:39,247 #include <...> search starts here: 2023-09-12T11:03:39,247 /usr/include/eigen3 2023-09-12T11:03:39,248 include 2023-09-12T11:03:39,249 /usr/include/python3.11 2023-09-12T11:03:39,249 /usr/include/c++/12 2023-09-12T11:03:39,250 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:39,250 /usr/include/c++/12/backward 2023-09-12T11:03:39,251 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:39,252 /usr/local/include 2023-09-12T11:03:39,252 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:39,253 /usr/include 2023-09-12T11:03:39,253 End of search list. 2023-09-12T11:03:39,254 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:39,255 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 2023-09-12T11:03:39,256 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:39,256 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:39,257 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:40,818 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:40,818 from include/openbabel/mol.h:43, 2023-09-12T11:03:40,819 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:40,820 from ./src/formats/hinformat.cpp:17: 2023-09-12T11:03:40,820 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:40,821 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:40,821 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:40,822 | ^ 2023-09-12T11:03:40,822 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:40,823 37 | # define UNUSED(x) x 2023-09-12T11:03:40,823 | ^ 2023-09-12T11:03:41,584 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:41,584 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:41,585 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:41,586 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:41,586 | ^ 2023-09-12T11:03:41,587 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:41,587 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:41,588 | ^~~~~~~~ 2023-09-12T11:03:41,589 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:41,590 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:41,591 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:41,591 | ^ 2023-09-12T11:03:41,592 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:41,593 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:41,594 | ^~~~~~~~ 2023-09-12T11:03:41,608 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:41,609 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:41,609 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:41,610 | ^ 2023-09-12T11:03:41,611 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:41,611 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:41,612 | ^~~~~~~~ 2023-09-12T11:03:41,614 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:41,615 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:41,616 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:41,617 | ^ 2023-09-12T11:03:41,618 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:41,618 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:41,619 | ^~~~~~~~ 2023-09-12T11:03:41,787 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:41,788 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:41,788 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:41,789 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:41,789 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:41,790 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:41,791 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:41,791 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:41,792 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:41,792 from include/openbabel/mol.h:35: 2023-09-12T11:03:41,793 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:41,794 131 | struct binary_function 2023-09-12T11:03:41,794 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:44,614 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/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/' 2023-09-12T11:03:44,615 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/ccHoVToD.s 2023-09-12T11:03:44,619 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:44,786 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/ 2023-09-12T11:03:44,786 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/ 2023-09-12T11:03:44,787 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:03:44,788 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 2023-09-12T11:03:44,792 Using built-in specs. 2023-09-12T11:03:44,793 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:44,793 Target: arm-linux-gnueabihf 2023-09-12T11:03:44,794 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 2023-09-12T11:03:44,794 Thread model: posix 2023-09-12T11:03:44,795 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:44,795 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:44,796 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:44,796 /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/ccsuMpfQ.s 2023-09-12T11:03:44,805 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:44,806 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:44,807 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:44,808 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:44,808 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:44,809 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:44,809 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:44,810 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:44,811 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:44,811 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:44,812 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:44,812 #include "..." search starts here: 2023-09-12T11:03:44,813 #include <...> search starts here: 2023-09-12T11:03:44,814 /usr/include/eigen3 2023-09-12T11:03:44,814 include 2023-09-12T11:03:44,815 /usr/include/python3.11 2023-09-12T11:03:44,815 /usr/include/c++/12 2023-09-12T11:03:44,816 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:44,816 /usr/include/c++/12/backward 2023-09-12T11:03:44,816 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:44,817 /usr/local/include 2023-09-12T11:03:44,817 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:44,818 /usr/include 2023-09-12T11:03:44,818 End of search list. 2023-09-12T11:03:44,819 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:44,819 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 2023-09-12T11:03:44,820 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:44,820 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:44,825 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:46,398 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:46,398 from include/openbabel/mol.h:43, 2023-09-12T11:03:46,399 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:46,399 from ./src/formats/jaguarformat.cpp:17: 2023-09-12T11:03:46,400 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:46,400 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:46,401 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:46,402 | ^ 2023-09-12T11:03:46,402 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:46,403 37 | # define UNUSED(x) x 2023-09-12T11:03:46,403 | ^ 2023-09-12T11:03:47,176 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:47,176 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,177 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,178 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:47,178 | ^ 2023-09-12T11:03:47,179 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:47,180 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:47,181 | ^~~~~~~~ 2023-09-12T11:03:47,182 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,182 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,183 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:47,184 | ^ 2023-09-12T11:03:47,184 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:47,185 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:47,186 | ^~~~~~~~ 2023-09-12T11:03:47,201 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,202 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,203 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:47,203 | ^ 2023-09-12T11:03:47,204 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:47,205 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:47,205 | ^~~~~~~~ 2023-09-12T11:03:47,209 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:47,210 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:47,210 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:47,211 | ^ 2023-09-12T11:03:47,211 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:47,212 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:47,212 | ^~~~~~~~ 2023-09-12T11:03:47,383 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:47,384 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:47,384 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:47,385 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:47,386 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:47,387 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:47,387 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:47,388 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:47,389 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:47,389 from include/openbabel/mol.h:35: 2023-09-12T11:03:47,390 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:47,391 131 | struct binary_function 2023-09-12T11:03:47,391 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:50,902 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:50,902 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/jaguarformat.o /tmp/ccsuMpfQ.s 2023-09-12T11:03:50,907 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:03:51,130 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/ 2023-09-12T11:03:51,131 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/ 2023-09-12T11:03:51,131 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/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.' 2023-09-12T11:03:51,133 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 2023-09-12T11:03:51,137 Using built-in specs. 2023-09-12T11:03:51,137 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:03:51,138 Target: arm-linux-gnueabihf 2023-09-12T11:03:51,138 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 2023-09-12T11:03:51,139 Thread model: posix 2023-09-12T11:03:51,140 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:03:51,140 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:03:51,141 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:03:51,141 /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/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/ccCx8qdX.s 2023-09-12T11:03:51,150 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:51,151 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:03:51,152 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:51,152 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:51,152 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:03:51,153 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:03:51,153 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:03:51,154 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:03:51,154 ignoring duplicate directory "/usr/include/" 2023-09-12T11:03:51,155 as it is a non-system directory that duplicates a system directory 2023-09-12T11:03:51,155 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:03:51,155 #include "..." search starts here: 2023-09-12T11:03:51,156 #include <...> search starts here: 2023-09-12T11:03:51,156 /usr/include/eigen3 2023-09-12T11:03:51,157 include 2023-09-12T11:03:51,157 /usr/include/python3.11 2023-09-12T11:03:51,157 /usr/include/c++/12 2023-09-12T11:03:51,158 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:03:51,158 /usr/include/c++/12/backward 2023-09-12T11:03:51,159 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:03:51,159 /usr/local/include 2023-09-12T11:03:51,160 /usr/include/arm-linux-gnueabihf 2023-09-12T11:03:51,160 /usr/include 2023-09-12T11:03:51,161 End of search list. 2023-09-12T11:03:51,161 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:03:51,162 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 2023-09-12T11:03:51,163 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:03:51,164 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:03:51,168 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:03:52,733 In file included from include/openbabel/atom.h:33, 2023-09-12T11:03:52,734 from include/openbabel/mol.h:43, 2023-09-12T11:03:52,735 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:03:52,736 from ./src/formats/lmpdatformat.cpp:15: 2023-09-12T11:03:52,736 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:03:52,737 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:03:52,738 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:03:52,738 | ^ 2023-09-12T11:03:52,739 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:03:52,740 37 | # define UNUSED(x) x 2023-09-12T11:03:52,740 | ^ 2023-09-12T11:03:53,501 In file included from include/openbabel/mol.h:52: 2023-09-12T11:03:53,501 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:53,502 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:53,503 862 | {return new OBVibrationData(*this);} 2023-09-12T11:03:53,504 | ^ 2023-09-12T11:03:53,504 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:03:53,505 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:03:53,506 | ^~~~~~~~ 2023-09-12T11:03:53,507 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:53,507 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:53,508 907 | {return new OBDOSData(*this);} 2023-09-12T11:03:53,508 | ^ 2023-09-12T11:03:53,509 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:03:53,510 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:03:53,510 | ^~~~~~~~ 2023-09-12T11:03:53,525 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:53,525 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:53,526 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:03:53,527 | ^ 2023-09-12T11:03:53,527 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:03:53,528 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:03:53,529 | ^~~~~~~~ 2023-09-12T11:03:53,531 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:03:53,532 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:03:53,533 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:03:53,533 | ^ 2023-09-12T11:03:53,534 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:03:53,535 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:03:53,536 | ^~~~~~~~ 2023-09-12T11:03:53,704 In file included from include/openbabel/format.h:22, 2023-09-12T11:03:53,705 from include/openbabel/obconversion.h:37, 2023-09-12T11:03:53,705 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:03:53,706 include/openbabel/plugin.h: At global scope: 2023-09-12T11:03:53,707 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:03:53,707 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:03:53,708 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:53,709 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:03:53,710 from /usr/include/c++/12/vector:66, 2023-09-12T11:03:53,711 from include/openbabel/mol.h:35: 2023-09-12T11:03:53,711 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:03:53,712 131 | struct binary_function 2023-09-12T11:03:53,712 | ^~~~~~~~~~~~~~~ 2023-09-12T11:03:53,977 ./src/formats/lmpdatformat.cpp: In member function ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:03:53,978 ./src/formats/lmpdatformat.cpp:271:20: warning: unused variable ‘length’ [-Wunused-variable] 2023-09-12T11:03:53,978 271 | double length=cmax-cmin; 2023-09-12T11:03:53,979 | ^~~~~~ 2023-09-12T11:03:54,013 ./src/formats/lmpdatformat.cpp:361:25: warning: unused variable ‘atomid’ [-Wunused-variable] 2023-09-12T11:03:54,014 361 | int atomid=5; 2023-09-12T11:03:54,015 | ^~~~~~ 2023-09-12T11:03:54,015 ./src/formats/lmpdatformat.cpp:362:28: warning: unused variable ‘charge’ [-Wunused-variable] 2023-09-12T11:03:54,016 362 | double charge=0.5; 2023-09-12T11:03:54,016 | ^~~~~~ 2023-09-12T11:03:57,351 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:03:57,352 from include/openbabel/mol.h:37: 2023-09-12T11:03:57,352 /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> >]’: 2023-09-12T11:03:57,353 /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 2023-09-12T11:03:57,354 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:03:57,354 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:57,462 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:03:57,463 /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> >]’: 2023-09-12T11:03:57,464 /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 2023-09-12T11:03:57,464 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:03:57,465 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:57,466 512 | std::tuple(__k), 2023-09-12T11:03:57,466 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:57,467 513 | std::tuple<>()); 2023-09-12T11:03:57,468 | ~~~~~~~~~~~~~~~ 2023-09-12T11:03:58,821 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> >]’, 2023-09-12T11:03:58,821 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:98:21: 2023-09-12T11:03:58,822 /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 2023-09-12T11:03:58,823 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:03:58,823 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:58,824 512 | std::tuple(__k), 2023-09-12T11:03:58,824 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:58,825 513 | std::tuple<>()); 2023-09-12T11:03:58,825 | ~~~~~~~~~~~~~~~ 2023-09-12T11:03:58,841 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> >]’, 2023-09-12T11:03:58,841 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:368:28: 2023-09-12T11:03:58,842 /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 2023-09-12T11:03:58,843 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:03:58,844 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:58,845 512 | std::tuple(__k), 2023-09-12T11:03:58,845 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:03:58,846 513 | std::tuple<>()); 2023-09-12T11:03:58,847 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:01,569 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:04:01,569 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/ccCx8qdX.s 2023-09-12T11:04:01,577 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:02,106 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/ 2023-09-12T11:04:02,106 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/ 2023-09-12T11:04:02,107 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:04:02,109 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 2023-09-12T11:04:02,114 Using built-in specs. 2023-09-12T11:04:02,114 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:02,115 Target: arm-linux-gnueabihf 2023-09-12T11:04:02,115 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 2023-09-12T11:04:02,116 Thread model: posix 2023-09-12T11:04:02,117 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:02,117 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:02,118 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:04:02,118 /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/ccd1rMur.s 2023-09-12T11:04:02,127 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:02,128 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:02,129 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:02,129 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:02,130 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:02,130 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:02,130 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:02,131 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:02,131 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:02,132 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:02,132 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:02,133 #include "..." search starts here: 2023-09-12T11:04:02,134 #include <...> search starts here: 2023-09-12T11:04:02,134 /usr/include/eigen3 2023-09-12T11:04:02,135 include 2023-09-12T11:04:02,135 /usr/include/python3.11 2023-09-12T11:04:02,137 /usr/include/c++/12 2023-09-12T11:04:02,137 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:02,138 /usr/include/c++/12/backward 2023-09-12T11:04:02,139 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:02,139 /usr/local/include 2023-09-12T11:04:02,140 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:02,141 /usr/include 2023-09-12T11:04:02,141 End of search list. 2023-09-12T11:04:02,142 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:02,142 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:02,144 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:02,144 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:02,146 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:03,708 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:03,708 from include/openbabel/mol.h:43, 2023-09-12T11:04:03,709 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:03,710 from ./src/formats/lpmdformat.cpp:15: 2023-09-12T11:04:03,710 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:03,711 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:03,712 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:03,712 | ^ 2023-09-12T11:04:03,713 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:03,714 37 | # define UNUSED(x) x 2023-09-12T11:04:03,714 | ^ 2023-09-12T11:04:04,475 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:04,475 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:04,476 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:04,477 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:04,477 | ^ 2023-09-12T11:04:04,478 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:04,478 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:04,479 | ^~~~~~~~ 2023-09-12T11:04:04,480 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:04,480 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:04,481 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:04,482 | ^ 2023-09-12T11:04:04,482 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:04,483 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:04,483 | ^~~~~~~~ 2023-09-12T11:04:04,499 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:04,499 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:04,500 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:04,501 | ^ 2023-09-12T11:04:04,502 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:04,502 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:04,503 | ^~~~~~~~ 2023-09-12T11:04:04,505 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:04,506 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:04,507 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:04,507 | ^ 2023-09-12T11:04:04,508 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:04,509 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:04,509 | ^~~~~~~~ 2023-09-12T11:04:04,678 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:04,679 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:04,680 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:04,680 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:04,681 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:04,683 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:04,683 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:04,684 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:04,684 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:04,685 from include/openbabel/mol.h:35: 2023-09-12T11:04:04,685 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:04,686 131 | struct binary_function 2023-09-12T11:04:04,686 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:04,894 ./src/formats/lpmdformat.cpp: In member function ‘virtual int OpenBabel::LpmdFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:04:04,895 ./src/formats/lpmdformat.cpp:56:31: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:04:04,895 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:04:04,896 | ~~~~^ 2023-09-12T11:04:04,897 ./src/formats/lpmdformat.cpp:56:48: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:04,897 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:04:04,898 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:04,901 ./src/formats/lpmdformat.cpp: In member function ‘bool OpenBabel::LpmdFormat::ReadHeader(std::istream&, OpenBabel::OBMol&)’: 2023-09-12T11:04:04,902 ./src/formats/lpmdformat.cpp:91:56: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T11:04:04,902 91 | bool LpmdFormat::ReadHeader( std::istream &ifs, OBMol &mol ) 2023-09-12T11:04:04,903 | ~~~~~~~^~~ 2023-09-12T11:04:04,907 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:04,908 ./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] 2023-09-12T11:04:04,909 190 | if(int(headers.size()-1)!=tokens.size()) 2023-09-12T11:04:04,909 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T11:04:04,912 ./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] 2023-09-12T11:04:04,913 204 | for(int i=1 ; i < headers.size() ; ++i) //the first element is HDR 2023-09-12T11:04:04,913 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T11:04:04,919 ./src/formats/lpmdformat.cpp:237:11: warning: unused variable ‘FX’ [-Wunused-variable] 2023-09-12T11:04:04,920 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2023-09-12T11:04:04,920 | ^~ 2023-09-12T11:04:04,921 ./src/formats/lpmdformat.cpp:237:32: warning: unused variable ‘FY’ [-Wunused-variable] 2023-09-12T11:04:04,922 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2023-09-12T11:04:04,922 | ^~ 2023-09-12T11:04:04,923 ./src/formats/lpmdformat.cpp:237:53: warning: unused variable ‘FZ’ [-Wunused-variable] 2023-09-12T11:04:04,924 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2023-09-12T11:04:04,924 | ^~ 2023-09-12T11:04:04,938 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:04,938 ./src/formats/lpmdformat.cpp:360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:04:04,939 360 | for(int i=0; i < mol.NumAtoms() ; ++i) 2023-09-12T11:04:04,940 | ~~^~~~~~~~~~~~~~~~ 2023-09-12T11:04:04,941 ./src/formats/lpmdformat.cpp:376:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:04:04,942 376 | for(int i=0;i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’: 2023-09-12T11:04:08,590 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:04:08,590 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:04:08,591 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:09,636 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:09,636 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, 2023-09-12T11:04:09,637 inlined from ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:239:19: 2023-09-12T11:04:09,637 /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 2023-09-12T11:04:09,638 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:09,639 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:09,639 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:09,640 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, 2023-09-12T11:04:09,641 inlined from ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:240:19: 2023-09-12T11:04:09,642 /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 2023-09-12T11:04:09,642 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:09,643 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:11,792 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:11,793 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, 2023-09-12T11:04:11,794 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:300:14: 2023-09-12T11:04:11,794 /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 2023-09-12T11:04:11,795 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:11,796 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:11,797 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:11,798 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, 2023-09-12T11:04:11,798 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:301:14: 2023-09-12T11:04:11,799 /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 2023-09-12T11:04:11,799 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:11,800 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:11,800 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:11,801 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, 2023-09-12T11:04:11,802 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:302:14: 2023-09-12T11:04:11,802 /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 2023-09-12T11:04:11,803 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:11,804 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:11,804 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:11,805 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, 2023-09-12T11:04:11,806 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:357:18: 2023-09-12T11:04:11,806 /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 2023-09-12T11:04:11,807 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:11,808 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:11,809 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:11,809 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, 2023-09-12T11:04:11,810 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:358:18: 2023-09-12T11:04:11,811 /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 2023-09-12T11:04:11,812 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:11,813 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:11,813 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:04:11,814 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, 2023-09-12T11:04:11,815 inlined from ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lpmdformat.cpp:359:18: 2023-09-12T11:04:11,815 /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 2023-09-12T11:04:11,816 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:04:11,817 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:13,451 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:04:13,451 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/ccd1rMur.s 2023-09-12T11:04:13,456 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:14,097 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/ 2023-09-12T11:04:14,098 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/ 2023-09-12T11:04:14,098 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:04:14,101 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 2023-09-12T11:04:14,105 Using built-in specs. 2023-09-12T11:04:14,106 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:14,107 Target: arm-linux-gnueabihf 2023-09-12T11:04:14,107 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 2023-09-12T11:04:14,107 Thread model: posix 2023-09-12T11:04:14,108 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:14,109 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:14,109 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:04:14,110 /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/ccW9uLGr.s 2023-09-12T11:04:14,118 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:14,118 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:14,120 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:14,120 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:14,121 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:14,121 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:14,122 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:14,123 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:14,123 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:14,124 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:14,124 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:14,125 #include "..." search starts here: 2023-09-12T11:04:14,126 #include <...> search starts here: 2023-09-12T11:04:14,126 /usr/include/eigen3 2023-09-12T11:04:14,127 include 2023-09-12T11:04:14,128 /usr/include/python3.11 2023-09-12T11:04:14,128 /usr/include/c++/12 2023-09-12T11:04:14,129 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:14,130 /usr/include/c++/12/backward 2023-09-12T11:04:14,131 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:14,131 /usr/local/include 2023-09-12T11:04:14,132 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:14,132 /usr/include 2023-09-12T11:04:14,132 End of search list. 2023-09-12T11:04:14,133 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:14,133 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:14,134 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:14,135 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:14,136 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:15,714 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:15,714 from include/openbabel/mol.h:43, 2023-09-12T11:04:15,715 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:15,716 from ./src/formats/mdffformat.cpp:17: 2023-09-12T11:04:15,716 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:15,717 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:15,717 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:15,718 | ^ 2023-09-12T11:04:15,718 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:15,719 37 | # define UNUSED(x) x 2023-09-12T11:04:15,720 | ^ 2023-09-12T11:04:16,482 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:16,491 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:16,492 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:16,492 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:16,493 | ^ 2023-09-12T11:04:16,494 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:16,494 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:16,495 | ^~~~~~~~ 2023-09-12T11:04:16,496 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:16,497 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:16,497 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:16,498 | ^ 2023-09-12T11:04:16,498 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:16,499 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:16,500 | ^~~~~~~~ 2023-09-12T11:04:16,505 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:16,506 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:16,507 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:16,508 | ^ 2023-09-12T11:04:16,509 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:16,509 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:16,510 | ^~~~~~~~ 2023-09-12T11:04:16,512 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:16,512 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:16,513 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:16,514 | ^ 2023-09-12T11:04:16,514 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:16,515 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:16,515 | ^~~~~~~~ 2023-09-12T11:04:16,686 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:16,686 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:16,687 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:16,688 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:16,688 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:16,689 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:16,690 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:16,691 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:16,691 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:16,692 from include/openbabel/mol.h:35: 2023-09-12T11:04:16,693 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:16,694 131 | struct binary_function 2023-09-12T11:04:16,694 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:17,007 ./src/formats/mdffformat.cpp: In member function ‘virtual int OpenBabel::MDFFFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:04:17,008 ./src/formats/mdffformat.cpp:71:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:04:17,009 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:04:17,009 | ~~~~^ 2023-09-12T11:04:17,010 ./src/formats/mdffformat.cpp:71:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:17,011 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:04:17,011 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:17,042 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:17,043 ./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] 2023-09-12T11:04:17,044 241 | for(int i = 0; i < atom_t_prop.size(); i++) 2023-09-12T11:04:17,045 | ~~^~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:17,046 ./src/formats/mdffformat.cpp:262:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:04:17,047 262 | for(unsigned int j = 0; j < atom_t_prop[i].num_of_atoms; j++) 2023-09-12T11:04:17,047 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:17,055 ./src/formats/mdffformat.cpp: In member function ‘bool OpenBabel::aindx::operator<(const OpenBabel::aindx&) const’: 2023-09-12T11:04:17,056 ./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] 2023-09-12T11:04:17,056 321 | for(int i = 0; i < vs.size(); i++) 2023-09-12T11:04:17,057 | ~~^~~~~~~~~~~ 2023-09-12T11:04:17,093 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:17,093 ./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] 2023-09-12T11:04:17,094 380 | for(int i = 0; i < vs.size(); i++) 2023-09-12T11:04:17,094 | ~~^~~~~~~~~~~ 2023-09-12T11:04:17,174 ./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] 2023-09-12T11:04:17,175 435 | for (int i = 0; i < atypes_def.size(); i++) 2023-09-12T11:04:17,176 | ~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:17,177 ./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] 2023-09-12T11:04:17,177 442 | for (int i = 0; i < atypes_def.size(); i++) 2023-09-12T11:04:17,178 | ~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:17,219 ./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] 2023-09-12T11:04:17,220 492 | for(int j = 0; j < atypes_def.size(); j++) 2023-09-12T11:04:17,221 | ~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:23,956 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:04:23,957 from include/openbabel/mol.h:37: 2023-09-12T11:04:23,958 /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> >]’: 2023-09-12T11:04:23,958 /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 2023-09-12T11:04:23,959 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:04:23,960 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,914 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:04:24,915 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> >]’, 2023-09-12T11:04:24,916 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:464:23: 2023-09-12T11:04:24,916 /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 2023-09-12T11:04:24,917 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:24,917 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,918 512 | std::tuple(__k), 2023-09-12T11:04:24,918 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,919 513 | std::tuple<>()); 2023-09-12T11:04:24,920 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,921 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> >]’, 2023-09-12T11:04:24,922 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:466:26: 2023-09-12T11:04:24,922 /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 2023-09-12T11:04:24,923 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:24,924 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,924 512 | std::tuple(__k), 2023-09-12T11:04:24,925 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,926 513 | std::tuple<>()); 2023-09-12T11:04:24,926 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,927 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> >]’, 2023-09-12T11:04:24,928 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:467:25: 2023-09-12T11:04:24,928 /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 2023-09-12T11:04:24,929 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:24,930 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,930 512 | std::tuple(__k), 2023-09-12T11:04:24,931 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,932 513 | std::tuple<>()); 2023-09-12T11:04:24,932 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,933 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> >]’, 2023-09-12T11:04:24,933 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:499:53: 2023-09-12T11:04:24,934 /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 2023-09-12T11:04:24,935 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:04:24,936 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,936 512 | std::tuple(__k), 2023-09-12T11:04:24,937 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:24,938 513 | std::tuple<>()); 2023-09-12T11:04:24,939 | ~~~~~~~~~~~~~~~ 2023-09-12T11:04:26,950 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:04:26,950 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/ccW9uLGr.s 2023-09-12T11:04:26,955 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:27,650 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/ 2023-09-12T11:04:27,651 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/ 2023-09-12T11:04:27,652 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:04:27,654 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 2023-09-12T11:04:27,658 Using built-in specs. 2023-09-12T11:04:27,659 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:27,660 Target: arm-linux-gnueabihf 2023-09-12T11:04:27,660 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 2023-09-12T11:04:27,661 Thread model: posix 2023-09-12T11:04:27,662 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:27,662 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:27,663 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:04:27,664 /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/ccPp748l.s 2023-09-12T11:04:27,671 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:27,672 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:27,673 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:27,674 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:27,674 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:27,674 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:27,675 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:27,675 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:27,676 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:27,676 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:27,677 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:27,677 #include "..." search starts here: 2023-09-12T11:04:27,678 #include <...> search starts here: 2023-09-12T11:04:27,678 /usr/include/eigen3 2023-09-12T11:04:27,679 include 2023-09-12T11:04:27,679 /usr/include/python3.11 2023-09-12T11:04:27,680 /usr/include/c++/12 2023-09-12T11:04:27,680 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:27,680 /usr/include/c++/12/backward 2023-09-12T11:04:27,681 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:27,681 /usr/local/include 2023-09-12T11:04:27,682 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:27,682 /usr/include 2023-09-12T11:04:27,683 End of search list. 2023-09-12T11:04:27,683 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:27,684 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 2023-09-12T11:04:27,685 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:27,686 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:27,690 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:29,482 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:29,483 from include/openbabel/mol.h:43, 2023-09-12T11:04:29,483 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:29,484 from ./src/formats/mdlformat.cpp:26: 2023-09-12T11:04:29,485 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:29,486 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:29,486 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:29,487 | ^ 2023-09-12T11:04:29,488 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:29,489 37 | # define UNUSED(x) x 2023-09-12T11:04:29,489 | ^ 2023-09-12T11:04:30,179 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:30,179 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:30,180 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:30,181 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:30,181 | ^ 2023-09-12T11:04:30,182 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:30,183 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:30,184 | ^~~~~~~~ 2023-09-12T11:04:30,185 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:30,185 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:30,186 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:30,187 | ^ 2023-09-12T11:04:30,187 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:30,188 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:30,188 | ^~~~~~~~ 2023-09-12T11:04:30,203 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:30,204 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:30,205 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:30,206 | ^ 2023-09-12T11:04:30,207 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:30,207 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:30,208 | ^~~~~~~~ 2023-09-12T11:04:30,209 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:30,210 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:30,211 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:30,211 | ^ 2023-09-12T11:04:30,212 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:30,213 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:30,214 | ^~~~~~~~ 2023-09-12T11:04:30,382 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:30,383 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:30,384 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:30,384 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:30,385 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:30,386 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:30,386 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:30,387 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:30,388 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:30,389 from ./src/formats/mdlformat.cpp:22: 2023-09-12T11:04:30,389 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:30,390 131 | struct binary_function 2023-09-12T11:04:30,391 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:30,949 In file included from ./src/formats/mdlformat.cpp:34: 2023-09-12T11:04:30,950 include/formats/mdlvalence.h: In function ‘unsigned int MDLValence(unsigned int, int, unsigned int)’: 2023-09-12T11:04:30,950 include/formats/mdlvalence.h:51:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,951 51 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,951 | ^~ 2023-09-12T11:04:30,952 include/formats/mdlvalence.h:51:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,952 51 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,953 | ^~~~~ 2023-09-12T11:04:30,953 include/formats/mdlvalence.h:64:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,954 64 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,954 | ^~ 2023-09-12T11:04:30,955 include/formats/mdlvalence.h:64:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,955 64 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,956 | ^~~~~ 2023-09-12T11:04:30,956 include/formats/mdlvalence.h:77:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,957 77 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,957 | ^~ 2023-09-12T11:04:30,958 include/formats/mdlvalence.h:77:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,958 77 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,959 | ^~~~~ 2023-09-12T11:04:30,960 include/formats/mdlvalence.h:90:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,960 90 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,961 | ^~ 2023-09-12T11:04:30,962 include/formats/mdlvalence.h:90:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,962 90 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,963 | ^~~~~ 2023-09-12T11:04:30,964 include/formats/mdlvalence.h:103:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,964 103 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,965 | ^~ 2023-09-12T11:04:30,966 include/formats/mdlvalence.h:103:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,966 103 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,967 | ^~~~~ 2023-09-12T11:04:30,968 include/formats/mdlvalence.h:116:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,968 116 | if (val <= 7) return 7; break; 2023-09-12T11:04:30,969 | ^~ 2023-09-12T11:04:30,970 include/formats/mdlvalence.h:116:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,970 116 | if (val <= 7) return 7; break; 2023-09-12T11:04:30,971 | ^~~~~ 2023-09-12T11:04:30,972 include/formats/mdlvalence.h:119:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,972 119 | if (val <= 6) return 6; break; 2023-09-12T11:04:30,973 | ^~ 2023-09-12T11:04:30,974 include/formats/mdlvalence.h:119:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,975 119 | if (val <= 6) return 6; break; 2023-09-12T11:04:30,976 | ^~~~~ 2023-09-12T11:04:30,976 include/formats/mdlvalence.h:121:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,977 121 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,977 | ^~ 2023-09-12T11:04:30,978 include/formats/mdlvalence.h:121:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,978 121 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,979 | ^~~~~ 2023-09-12T11:04:30,980 include/formats/mdlvalence.h:134:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,980 134 | if (val <= 7) return 7; break; 2023-09-12T11:04:30,981 | ^~ 2023-09-12T11:04:30,981 include/formats/mdlvalence.h:134:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,982 134 | if (val <= 7) return 7; break; 2023-09-12T11:04:30,982 | ^~~~~ 2023-09-12T11:04:30,983 include/formats/mdlvalence.h:137:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,984 137 | if (val <= 6) return 6; break; 2023-09-12T11:04:30,984 | ^~ 2023-09-12T11:04:30,985 include/formats/mdlvalence.h:137:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,986 137 | if (val <= 6) return 6; break; 2023-09-12T11:04:30,986 | ^~~~~ 2023-09-12T11:04:30,987 include/formats/mdlvalence.h:139:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,988 139 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,989 | ^~ 2023-09-12T11:04:30,989 include/formats/mdlvalence.h:139:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,990 139 | if (val <= 5) return 5; break; 2023-09-12T11:04:30,991 | ^~~~~ 2023-09-12T11:04:30,992 include/formats/mdlvalence.h:152:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,993 152 | if (val <= 7) return 7; break; 2023-09-12T11:04:30,993 | ^~ 2023-09-12T11:04:30,994 include/formats/mdlvalence.h:152:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,995 152 | if (val <= 7) return 7; break; 2023-09-12T11:04:30,995 | ^~~~~ 2023-09-12T11:04:30,996 include/formats/mdlvalence.h:155:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:30,997 155 | if (val <= 6) return 6; break; 2023-09-12T11:04:30,997 | ^~ 2023-09-12T11:04:30,998 include/formats/mdlvalence.h:155:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:30,999 155 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,000 | ^~~~~ 2023-09-12T11:04:31,001 include/formats/mdlvalence.h:157:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,002 157 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,002 | ^~ 2023-09-12T11:04:31,004 include/formats/mdlvalence.h:157:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,004 157 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,004 | ^~~~~ 2023-09-12T11:04:31,005 include/formats/mdlvalence.h:170:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,005 170 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,006 | ^~ 2023-09-12T11:04:31,007 include/formats/mdlvalence.h:170:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,007 170 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,008 | ^~~~~ 2023-09-12T11:04:31,008 include/formats/mdlvalence.h:173:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,009 173 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,009 | ^~ 2023-09-12T11:04:31,010 include/formats/mdlvalence.h:173:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,011 173 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,011 | ^~~~~ 2023-09-12T11:04:31,012 include/formats/mdlvalence.h:175:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,012 175 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,013 | ^~ 2023-09-12T11:04:31,013 include/formats/mdlvalence.h:175:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,014 175 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,015 | ^~~~~ 2023-09-12T11:04:31,016 include/formats/mdlvalence.h:188:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,016 188 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,017 | ^~ 2023-09-12T11:04:31,018 include/formats/mdlvalence.h:188:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,019 188 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,019 | ^~~~~ 2023-09-12T11:04:31,020 include/formats/mdlvalence.h:191:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,021 191 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,022 | ^~ 2023-09-12T11:04:31,022 include/formats/mdlvalence.h:191:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,023 191 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,024 | ^~~~~ 2023-09-12T11:04:31,025 include/formats/mdlvalence.h:193:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,025 193 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,026 | ^~ 2023-09-12T11:04:31,027 include/formats/mdlvalence.h:193:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,027 193 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,028 | ^~~~~ 2023-09-12T11:04:31,029 include/formats/mdlvalence.h:206:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,030 206 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,031 | ^~ 2023-09-12T11:04:31,032 include/formats/mdlvalence.h:206:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,032 206 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,033 | ^~~~~ 2023-09-12T11:04:31,033 include/formats/mdlvalence.h:209:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,034 209 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,034 | ^~ 2023-09-12T11:04:31,035 include/formats/mdlvalence.h:209:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,036 209 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,036 | ^~~~~ 2023-09-12T11:04:31,037 include/formats/mdlvalence.h:211:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,037 211 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,038 | ^~ 2023-09-12T11:04:31,038 include/formats/mdlvalence.h:211:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,039 211 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,039 | ^~~~~ 2023-09-12T11:04:31,040 include/formats/mdlvalence.h:223:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,040 223 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,041 | ^~ 2023-09-12T11:04:31,042 include/formats/mdlvalence.h:223:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,042 223 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,043 | ^~~~~ 2023-09-12T11:04:31,044 include/formats/mdlvalence.h:226:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,045 226 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,045 | ^~ 2023-09-12T11:04:31,046 include/formats/mdlvalence.h:226:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,047 226 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,048 | ^~~~~ 2023-09-12T11:04:31,048 include/formats/mdlvalence.h:228:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,049 228 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,050 | ^~ 2023-09-12T11:04:31,051 include/formats/mdlvalence.h:228:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,051 228 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,052 | ^~~~~ 2023-09-12T11:04:31,053 include/formats/mdlvalence.h:240:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,053 240 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,054 | ^~ 2023-09-12T11:04:31,055 include/formats/mdlvalence.h:240:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,056 240 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,056 | ^~~~~ 2023-09-12T11:04:31,057 include/formats/mdlvalence.h:243:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,058 243 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,059 | ^~ 2023-09-12T11:04:31,059 include/formats/mdlvalence.h:243:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,060 243 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,060 | ^~~~~ 2023-09-12T11:04:31,061 include/formats/mdlvalence.h:245:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,062 245 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,062 | ^~ 2023-09-12T11:04:31,063 include/formats/mdlvalence.h:245:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,063 245 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,064 | ^~~~~ 2023-09-12T11:04:31,065 include/formats/mdlvalence.h:257:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,065 257 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,066 | ^~ 2023-09-12T11:04:31,067 include/formats/mdlvalence.h:257:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,067 257 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,068 | ^~~~~ 2023-09-12T11:04:31,069 include/formats/mdlvalence.h:260:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,069 260 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,070 | ^~ 2023-09-12T11:04:31,071 include/formats/mdlvalence.h:260:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,072 260 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,072 | ^~~~~ 2023-09-12T11:04:31,073 include/formats/mdlvalence.h:262:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,074 262 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,075 | ^~ 2023-09-12T11:04:31,076 include/formats/mdlvalence.h:262:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,076 262 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,077 | ^~~~~ 2023-09-12T11:04:31,078 include/formats/mdlvalence.h:274:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,079 274 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,080 | ^~ 2023-09-12T11:04:31,080 include/formats/mdlvalence.h:274:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,081 274 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,081 | ^~~~~ 2023-09-12T11:04:31,082 include/formats/mdlvalence.h:277:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,083 277 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,084 | ^~ 2023-09-12T11:04:31,084 include/formats/mdlvalence.h:277:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,085 277 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,086 | ^~~~~ 2023-09-12T11:04:31,087 include/formats/mdlvalence.h:279:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,087 279 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,088 | ^~ 2023-09-12T11:04:31,089 include/formats/mdlvalence.h:279:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,089 279 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,090 | ^~~~~ 2023-09-12T11:04:31,090 include/formats/mdlvalence.h:291:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,091 291 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,091 | ^~ 2023-09-12T11:04:31,092 include/formats/mdlvalence.h:291:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,092 291 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,093 | ^~~~~ 2023-09-12T11:04:31,093 include/formats/mdlvalence.h:294:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,094 294 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,094 | ^~ 2023-09-12T11:04:31,095 include/formats/mdlvalence.h:294:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,095 294 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,096 | ^~~~~ 2023-09-12T11:04:31,096 include/formats/mdlvalence.h:296:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,097 296 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,097 | ^~ 2023-09-12T11:04:31,098 include/formats/mdlvalence.h:296:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,099 296 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,099 | ^~~~~ 2023-09-12T11:04:31,100 include/formats/mdlvalence.h:298:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,101 298 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,102 | ^~ 2023-09-12T11:04:31,103 include/formats/mdlvalence.h:298:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,103 298 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,104 | ^~~~~ 2023-09-12T11:04:31,105 include/formats/mdlvalence.h:310:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,105 310 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,106 | ^~ 2023-09-12T11:04:31,107 include/formats/mdlvalence.h:310:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,108 310 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,108 | ^~~~~ 2023-09-12T11:04:31,109 include/formats/mdlvalence.h:313:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,110 313 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,111 | ^~ 2023-09-12T11:04:31,111 include/formats/mdlvalence.h:313:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,112 313 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,113 | ^~~~~ 2023-09-12T11:04:31,114 include/formats/mdlvalence.h:315:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,115 315 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,115 | ^~ 2023-09-12T11:04:31,116 include/formats/mdlvalence.h:315:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,116 315 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,117 | ^~~~~ 2023-09-12T11:04:31,117 include/formats/mdlvalence.h:317:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,118 317 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,119 | ^~ 2023-09-12T11:04:31,119 include/formats/mdlvalence.h:317:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,120 317 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,121 | ^~~~~ 2023-09-12T11:04:31,121 include/formats/mdlvalence.h:329:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,122 329 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,122 | ^~ 2023-09-12T11:04:31,123 include/formats/mdlvalence.h:329:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,123 329 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,124 | ^~~~~ 2023-09-12T11:04:31,125 include/formats/mdlvalence.h:332:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,125 332 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,126 | ^~ 2023-09-12T11:04:31,127 include/formats/mdlvalence.h:332:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,128 332 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,128 | ^~~~~ 2023-09-12T11:04:31,129 include/formats/mdlvalence.h:334:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,130 334 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,131 | ^~ 2023-09-12T11:04:31,132 include/formats/mdlvalence.h:334:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,132 334 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,133 | ^~~~~ 2023-09-12T11:04:31,134 include/formats/mdlvalence.h:336:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,134 336 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,135 | ^~ 2023-09-12T11:04:31,136 include/formats/mdlvalence.h:336:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,137 336 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,137 | ^~~~~ 2023-09-12T11:04:31,138 include/formats/mdlvalence.h:348:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,139 348 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,140 | ^~ 2023-09-12T11:04:31,140 include/formats/mdlvalence.h:348:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,141 348 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,142 | ^~~~~ 2023-09-12T11:04:31,143 include/formats/mdlvalence.h:351:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,144 351 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,144 | ^~ 2023-09-12T11:04:31,145 include/formats/mdlvalence.h:351:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,145 351 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,146 | ^~~~~ 2023-09-12T11:04:31,146 include/formats/mdlvalence.h:353:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,147 353 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,148 | ^~ 2023-09-12T11:04:31,148 include/formats/mdlvalence.h:353:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,149 353 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,149 | ^~~~~ 2023-09-12T11:04:31,150 include/formats/mdlvalence.h:355:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,150 355 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,151 | ^~ 2023-09-12T11:04:31,152 include/formats/mdlvalence.h:355:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,152 355 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,153 | ^~~~~ 2023-09-12T11:04:31,154 include/formats/mdlvalence.h:367:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,154 367 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,155 | ^~ 2023-09-12T11:04:31,156 include/formats/mdlvalence.h:367:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,157 367 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,158 | ^~~~~ 2023-09-12T11:04:31,158 include/formats/mdlvalence.h:370:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,159 370 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,160 | ^~ 2023-09-12T11:04:31,161 include/formats/mdlvalence.h:370:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,162 370 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,162 | ^~~~~ 2023-09-12T11:04:31,163 include/formats/mdlvalence.h:372:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,164 372 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,164 | ^~ 2023-09-12T11:04:31,165 include/formats/mdlvalence.h:372:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,166 372 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,166 | ^~~~~ 2023-09-12T11:04:31,167 include/formats/mdlvalence.h:374:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,168 374 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,169 | ^~ 2023-09-12T11:04:31,170 include/formats/mdlvalence.h:374:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,171 374 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,172 | ^~~~~ 2023-09-12T11:04:31,173 include/formats/mdlvalence.h:385:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,174 385 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,174 | ^~ 2023-09-12T11:04:31,175 include/formats/mdlvalence.h:385:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,176 385 | if (val <= 7) return 7; break; 2023-09-12T11:04:31,176 | ^~~~~ 2023-09-12T11:04:31,177 include/formats/mdlvalence.h:388:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,177 388 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,178 | ^~ 2023-09-12T11:04:31,178 include/formats/mdlvalence.h:388:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,179 388 | if (val <= 6) return 6; break; 2023-09-12T11:04:31,180 | ^~~~~ 2023-09-12T11:04:31,180 include/formats/mdlvalence.h:390:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,181 390 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,181 | ^~ 2023-09-12T11:04:31,182 include/formats/mdlvalence.h:390:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,183 390 | if (val <= 5) return 5; break; 2023-09-12T11:04:31,183 | ^~~~~ 2023-09-12T11:04:31,184 include/formats/mdlvalence.h:392:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,185 392 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,185 | ^~ 2023-09-12T11:04:31,186 include/formats/mdlvalence.h:392:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,187 392 | if (val <= 4) return 4; break; 2023-09-12T11:04:31,188 | ^~~~~ 2023-09-12T11:04:31,188 include/formats/mdlvalence.h:394:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:04:31,189 394 | if (val <= 3) return 3; break; 2023-09-12T11:04:31,190 | ^~ 2023-09-12T11:04:31,191 include/formats/mdlvalence.h:394:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:04:31,192 394 | if (val <= 3) return 3; break; 2023-09-12T11:04:31,192 | ^~~~~ 2023-09-12T11:04:31,193 include/formats/mdlvalence.h: In function ‘unsigned int HYDValence(unsigned int, int, unsigned int)’: 2023-09-12T11:04:31,194 include/formats/mdlvalence.h:416:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:04:31,194 416 | if (val > impval) { 2023-09-12T11:04:31,195 | ~~~~^~~~~~~~ 2023-09-12T11:04:31,462 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadV3000Block(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, bool)’: 2023-09-12T11:04:31,463 ./src/formats/mdlformat.cpp:1273:85: warning: unused parameter ‘DoMany’ [-Wunused-parameter] 2023-09-12T11:04:31,464 1273 | bool MDLFormat::ReadV3000Block(istream& ifs, OBMol& mol, OBConversion* pConv,bool DoMany) 2023-09-12T11:04:31,465 | ~~~~~^~~~~~ 2023-09-12T11:04:31,479 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadAtomBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:04:31,482 ./src/formats/mdlformat.cpp:1341:10: warning: unused variable ‘chiralWatch’ [-Wunused-variable] 2023-09-12T11:04:31,483 1341 | bool chiralWatch=false; 2023-09-12T11:04:31,484 | ^~~~~~~~~~~ 2023-09-12T11:04:31,484 ./src/formats/mdlformat.cpp:1338:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:31,485 1338 | bool MDLFormat::ReadAtomBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:04:31,485 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:31,486 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadBondBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:04:31,486 ./src/formats/mdlformat.cpp:1422:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:31,487 1422 | bool MDLFormat::ReadBondBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:04:31,488 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:31,488 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadUnimplementedBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, std::string&)’: 2023-09-12T11:04:31,489 ./src/formats/mdlformat.cpp:1481:62: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T11:04:31,489 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2023-09-12T11:04:31,490 | ~~~~~~~^~~ 2023-09-12T11:04:31,491 ./src/formats/mdlformat.cpp:1481:81: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:31,491 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2023-09-12T11:04:31,492 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:31,493 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadRGroupBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:04:31,494 ./src/formats/mdlformat.cpp:1497:55: warning: unused parameter ‘mol’ [-Wunused-parameter] 2023-09-12T11:04:31,495 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:04:31,496 | ~~~~~~~^~~ 2023-09-12T11:04:31,496 ./src/formats/mdlformat.cpp:1497:74: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:31,497 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:04:31,498 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:31,517 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::WriteV3000(std::ostream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2023-09-12T11:04:31,518 ./src/formats/mdlformat.cpp:1514:69: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:04:31,518 1514 | bool MDLFormat::WriteV3000(ostream& ofs,OBMol& mol, OBConversion* pConv) 2023-09-12T11:04:31,519 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:04:31,623 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2023-09-12T11:04:31,624 ./src/formats/mdlformat.cpp:1957:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:04:31,625 1957 | unsigned int second = (a1_b2 == NULL) ? OBStereo::ImplicitRef : a1_b2->GetNbrAtom(a1)->GetId(); 2023-09-12T11:04:31,626 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:31,627 ./src/formats/mdlformat.cpp:1958:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:04:31,627 1958 | unsigned int fourth = (a2_b2 == NULL) ? OBStereo::ImplicitRef : a2_b2->GetNbrAtom(a2)->GetId(); 2023-09-12T11:04:31,628 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:33,758 ./src/formats/mdlformat.cpp: In member function ‘virtual bool OpenBabel::MDLFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:33,759 ./src/formats/mdlformat.cpp:527:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T11:04:33,759 527 | flag |= OBBond::CisOrTrans; 2023-09-12T11:04:33,760 | ~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:33,760 ./src/formats/mdlformat.cpp:528:15: note: here 2023-09-12T11:04:33,761 528 | case 4: 2023-09-12T11:04:33,761 | ^~~~ 2023-09-12T11:04:39,983 ./src/formats/mdlformat.cpp: In member function ‘std::string OpenBabel::MDLFormat::GetTimeDate()’: 2023-09-12T11:04:39,983 ./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=] 2023-09-12T11:04:39,984 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2023-09-12T11:04:39,985 | ^~~~ 2023-09-12T11:04:39,985 ./src/formats/mdlformat.cpp:1648:22: note: directive argument in the range [-2147483648, 2147483547] 2023-09-12T11:04:39,986 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2023-09-12T11:04:39,987 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:39,987 ./src/formats/mdlformat.cpp:1648:13: note: ‘snprintf’ output between 11 and 56 bytes into a destination of size 11 2023-09-12T11:04:39,988 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2023-09-12T11:04:39,989 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:39,989 1649 | ((ts->tm_year>=100)? ts->tm_year-100 : ts->tm_year), 2023-09-12T11:04:39,990 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:39,991 1650 | ts->tm_hour, ts->tm_min); 2023-09-12T11:04:39,991 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:40,772 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2023-09-12T11:04:40,773 ./src/formats/mdlformat.cpp:1967:58: warning: ‘a2_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:04:40,773 1967 | if (a1_stereo == OBStereo::UnknownDir || a2_stereo == OBStereo::UnknownDir) 2023-09-12T11:04:40,774 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:40,775 ./src/formats/mdlformat.cpp:1926:42: note: ‘a2_stereo’ was declared here 2023-09-12T11:04:40,775 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2023-09-12T11:04:40,776 | ^~~~~~~~~ 2023-09-12T11:04:40,777 ./src/formats/mdlformat.cpp:1967:21: warning: ‘a1_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:04:40,777 1967 | if (a1_stereo == OBStereo::UnknownDir || a2_stereo == OBStereo::UnknownDir) 2023-09-12T11:04:40,778 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:04:40,779 ./src/formats/mdlformat.cpp:1926:31: note: ‘a1_stereo’ was declared here 2023-09-12T11:04:40,780 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2023-09-12T11:04:40,780 | ^~~~~~~~~ 2023-09-12T11:04:51,314 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/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/' 2023-09-12T11:04:51,315 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/mdlformat.o /tmp/ccPp748l.s 2023-09-12T11:04:51,319 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:04:52,846 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/ 2023-09-12T11:04:52,851 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/ 2023-09-12T11:04:52,851 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:04:52,854 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 2023-09-12T11:04:52,859 Using built-in specs. 2023-09-12T11:04:52,860 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:04:52,861 Target: arm-linux-gnueabihf 2023-09-12T11:04:52,862 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 2023-09-12T11:04:52,863 Thread model: posix 2023-09-12T11:04:52,864 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:04:52,865 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:04:52,865 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:04:52,866 /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/ccYIEyqE.s 2023-09-12T11:04:52,875 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:52,876 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:52,877 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:52,878 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:52,878 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:04:52,879 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:04:52,879 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:04:52,880 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:04:52,880 ignoring duplicate directory "/usr/include/" 2023-09-12T11:04:52,881 as it is a non-system directory that duplicates a system directory 2023-09-12T11:04:52,882 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:04:52,882 #include "..." search starts here: 2023-09-12T11:04:52,883 #include <...> search starts here: 2023-09-12T11:04:52,884 /usr/include/eigen3 2023-09-12T11:04:52,885 include 2023-09-12T11:04:52,885 /usr/include/python3.11 2023-09-12T11:04:52,886 /usr/include/c++/12 2023-09-12T11:04:52,887 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:04:52,888 /usr/include/c++/12/backward 2023-09-12T11:04:52,889 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:04:52,889 /usr/local/include 2023-09-12T11:04:52,890 /usr/include/arm-linux-gnueabihf 2023-09-12T11:04:52,891 /usr/include 2023-09-12T11:04:52,891 End of search list. 2023-09-12T11:04:52,892 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:04:52,893 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:04:52,894 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:04:52,895 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:04:52,896 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:04:54,501 In file included from include/openbabel/atom.h:33, 2023-09-12T11:04:54,502 from include/openbabel/mol.h:43, 2023-09-12T11:04:54,502 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:04:54,503 from ./src/formats/mmcifformat.cpp:19: 2023-09-12T11:04:54,504 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:04:54,504 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:04:54,505 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:04:54,506 | ^ 2023-09-12T11:04:54,507 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:04:54,507 37 | # define UNUSED(x) x 2023-09-12T11:04:54,508 | ^ 2023-09-12T11:04:55,270 In file included from include/openbabel/mol.h:52: 2023-09-12T11:04:55,270 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:55,271 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:55,271 862 | {return new OBVibrationData(*this);} 2023-09-12T11:04:55,272 | ^ 2023-09-12T11:04:55,272 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:04:55,273 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:04:55,274 | ^~~~~~~~ 2023-09-12T11:04:55,276 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:55,276 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:55,277 907 | {return new OBDOSData(*this);} 2023-09-12T11:04:55,278 | ^ 2023-09-12T11:04:55,278 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:04:55,279 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:04:55,280 | ^~~~~~~~ 2023-09-12T11:04:55,296 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:55,297 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:55,297 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:04:55,298 | ^ 2023-09-12T11:04:55,299 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:04:55,300 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:04:55,301 | ^~~~~~~~ 2023-09-12T11:04:55,303 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:04:55,304 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:04:55,305 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:04:55,305 | ^ 2023-09-12T11:04:55,306 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:04:55,307 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:04:55,308 | ^~~~~~~~ 2023-09-12T11:04:55,477 In file included from include/openbabel/format.h:22, 2023-09-12T11:04:55,478 from include/openbabel/obconversion.h:37, 2023-09-12T11:04:55,478 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:04:55,479 include/openbabel/plugin.h: At global scope: 2023-09-12T11:04:55,479 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:04:55,480 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:04:55,480 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:55,481 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:04:55,481 from /usr/include/c++/12/vector:66, 2023-09-12T11:04:55,482 from include/openbabel/mol.h:35: 2023-09-12T11:04:55,482 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:04:55,483 131 | struct binary_function 2023-09-12T11:04:55,483 | ^~~~~~~~~~~~~~~ 2023-09-12T11:04:57,538 ./src/formats/mmcifformat.cpp: In member function ‘bool OpenBabel::CIFLexer::next_token(Token&)’: 2023-09-12T11:04:57,538 ./src/formats/mmcifformat.cpp:394:8: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T11:04:57,539 394 | if (last_char == '\n') 2023-09-12T11:04:57,539 | ^~ 2023-09-12T11:04:57,540 ./src/formats/mmcifformat.cpp:421:6: note: here 2023-09-12T11:04:57,541 421 | default: // reading an un-quoted text string 2023-09-12T11:04:57,541 | ^~~~~~~ 2023-09-12T11:04:57,547 ./src/formats/mmcifformat.cpp: In member function ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:04:57,548 ./src/formats/mmcifformat.cpp:638:16: warning: this statement may fall through [-Wimplicit-fallthrough=] 2023-09-12T11:04:57,549 638 | if(string::npos != token.as_text.find_first_of("0123456789")) 2023-09-12T11:04:57,549 | ^~ 2023-09-12T11:04:57,550 ./src/formats/mmcifformat.cpp:640:14: note: here 2023-09-12T11:04:57,551 640 | case CIFTagID::_atom_site_type_symbol: 2023-09-12T11:04:57,552 | ^~~~ 2023-09-12T11:05:03,163 In file included from /usr/include/c++/12/map:60, 2023-09-12T11:05:03,163 from include/openbabel/mol.h:37: 2023-09-12T11:05:03,164 /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> >]’: 2023-09-12T11:05:03,165 /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 2023-09-12T11:05:03,165 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-12T11:05:03,166 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:04,261 In file included from /usr/include/c++/12/map:61: 2023-09-12T11:05:04,261 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> >]’, 2023-09-12T11:05:04,262 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:846:41: 2023-09-12T11:05:04,262 /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 2023-09-12T11:05:04,263 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:05:04,264 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:04,264 512 | std::tuple(__k), 2023-09-12T11:05:04,265 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:04,265 513 | std::tuple<>()); 2023-09-12T11:05:04,266 | ~~~~~~~~~~~~~~~ 2023-09-12T11:05:04,267 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> >]’, 2023-09-12T11:05:04,268 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:981:66: 2023-09-12T11:05:04,268 /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 2023-09-12T11:05:04,269 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-12T11:05:04,270 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:04,271 512 | std::tuple(__k), 2023-09-12T11:05:04,271 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:04,272 513 | std::tuple<>()); 2023-09-12T11:05:04,273 | ~~~~~~~~~~~~~~~ 2023-09-12T11:05:06,732 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:06,733 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/ccYIEyqE.s 2023-09-12T11:05:06,741 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:07,549 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/ 2023-09-12T11:05:07,550 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/ 2023-09-12T11:05:07,550 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:05:07,553 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 2023-09-12T11:05:07,558 Using built-in specs. 2023-09-12T11:05:07,559 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:07,559 Target: arm-linux-gnueabihf 2023-09-12T11:05:07,560 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 2023-09-12T11:05:07,560 Thread model: posix 2023-09-12T11:05:07,561 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:07,561 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:07,562 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:07,562 /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/cc78Daft.s 2023-09-12T11:05:07,572 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:07,573 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 2023-09-12T11:05:07,573 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:07,574 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:07,574 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:07,575 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:07,575 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:07,576 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:07,576 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:07,576 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:07,577 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:07,577 #include "..." search starts here: 2023-09-12T11:05:07,578 #include <...> search starts here: 2023-09-12T11:05:07,578 /usr/include/eigen3 2023-09-12T11:05:07,579 include 2023-09-12T11:05:07,579 /usr/include/python3.11 2023-09-12T11:05:07,580 /usr/include/c++/12 2023-09-12T11:05:07,580 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:07,581 /usr/include/c++/12/backward 2023-09-12T11:05:07,582 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:07,582 /usr/local/include 2023-09-12T11:05:07,583 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:07,583 /usr/include 2023-09-12T11:05:07,584 End of search list. 2023-09-12T11:05:07,585 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:07,585 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:07,587 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:07,587 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:07,593 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:09,153 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:09,154 from include/openbabel/mol.h:43, 2023-09-12T11:05:09,154 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:09,155 from ./src/formats/mmodformat.cpp:17: 2023-09-12T11:05:09,156 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:09,156 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:09,157 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:09,158 | ^ 2023-09-12T11:05:09,158 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:09,159 37 | # define UNUSED(x) x 2023-09-12T11:05:09,160 | ^ 2023-09-12T11:05:09,922 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:09,923 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:09,923 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:09,924 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:09,925 | ^ 2023-09-12T11:05:09,926 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:09,926 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:09,927 | ^~~~~~~~ 2023-09-12T11:05:09,928 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:09,929 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:09,929 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:09,930 | ^ 2023-09-12T11:05:09,931 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:09,931 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:09,932 | ^~~~~~~~ 2023-09-12T11:05:09,948 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:09,949 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:09,949 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:09,950 | ^ 2023-09-12T11:05:09,951 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:09,951 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:09,952 | ^~~~~~~~ 2023-09-12T11:05:09,956 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:09,956 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:09,957 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:09,958 | ^ 2023-09-12T11:05:09,959 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:09,959 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:09,960 | ^~~~~~~~ 2023-09-12T11:05:10,130 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:10,130 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:10,131 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:10,132 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:10,132 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:10,133 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:10,134 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:10,135 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:10,136 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:10,136 from include/openbabel/mol.h:35: 2023-09-12T11:05:10,137 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:10,137 131 | struct binary_function 2023-09-12T11:05:10,137 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:13,819 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:13,820 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/cc78Daft.s 2023-09-12T11:05:13,824 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:14,052 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/ 2023-09-12T11:05:14,053 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/ 2023-09-12T11:05:14,053 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:05:14,055 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 2023-09-12T11:05:14,058 Using built-in specs. 2023-09-12T11:05:14,059 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:14,060 Target: arm-linux-gnueabihf 2023-09-12T11:05:14,060 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 2023-09-12T11:05:14,061 Thread model: posix 2023-09-12T11:05:14,062 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:14,062 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:14,062 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:14,063 /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/ccHSZ5d6.s 2023-09-12T11:05:14,071 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:14,072 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:14,073 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:14,074 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:14,074 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:14,075 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:14,075 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:14,076 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:14,077 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:14,077 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:14,078 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:14,079 #include "..." search starts here: 2023-09-12T11:05:14,079 #include <...> search starts here: 2023-09-12T11:05:14,080 /usr/include/eigen3 2023-09-12T11:05:14,080 include 2023-09-12T11:05:14,081 /usr/include/python3.11 2023-09-12T11:05:14,081 /usr/include/c++/12 2023-09-12T11:05:14,082 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:14,082 /usr/include/c++/12/backward 2023-09-12T11:05:14,083 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:14,084 /usr/local/include 2023-09-12T11:05:14,084 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:14,085 /usr/include 2023-09-12T11:05:14,085 End of search list. 2023-09-12T11:05:14,086 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:14,086 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:14,087 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:14,088 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:14,089 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:15,651 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:15,652 from include/openbabel/mol.h:43, 2023-09-12T11:05:15,652 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:15,653 from ./src/formats/mol2format.cpp:17: 2023-09-12T11:05:15,653 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:15,654 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:15,654 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:15,655 | ^ 2023-09-12T11:05:15,655 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:15,656 37 | # define UNUSED(x) x 2023-09-12T11:05:15,656 | ^ 2023-09-12T11:05:16,418 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:16,418 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:16,419 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:16,420 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:16,420 | ^ 2023-09-12T11:05:16,421 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:16,421 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:16,422 | ^~~~~~~~ 2023-09-12T11:05:16,423 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:16,424 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:16,424 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:16,425 | ^ 2023-09-12T11:05:16,426 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:16,427 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:16,427 | ^~~~~~~~ 2023-09-12T11:05:16,442 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:16,443 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:16,443 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:16,444 | ^ 2023-09-12T11:05:16,445 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:16,445 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:16,446 | ^~~~~~~~ 2023-09-12T11:05:16,448 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:16,449 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:16,450 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:16,451 | ^ 2023-09-12T11:05:16,452 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:16,452 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:16,453 | ^~~~~~~~ 2023-09-12T11:05:16,621 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:16,622 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:16,622 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:16,623 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:16,623 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:16,624 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:16,625 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:16,625 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:16,626 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:16,626 from include/openbabel/mol.h:35: 2023-09-12T11:05:16,627 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:16,627 131 | struct binary_function 2023-09-12T11:05:16,628 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:16,821 ./src/formats/mol2format.cpp: In member function ‘virtual const char* OpenBabel::MOL2Format::Description()’: 2023-09-12T11:05:16,822 ./src/formats/mol2format.cpp:49:9: warning: statement has no effect [-Wunused-value] 2023-09-12T11:05:16,823 49 | " c Write UCSF Dock scores saved in comments preceeding molecules\n\n"; 2023-09-12T11:05:16,824 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:16,854 ./src/formats/mol2format.cpp: In member function ‘virtual bool OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:16,855 ./src/formats/mol2format.cpp:391:46: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:05:16,855 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2023-09-12T11:05:16,856 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:05:16,857 ./src/formats/mol2format.cpp:391:87: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:05:16,858 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2023-09-12T11:05:16,858 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:05:16,859 ./src/formats/mol2format.cpp:394:51: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:05:16,860 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2023-09-12T11:05:16,860 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:05:16,861 ./src/formats/mol2format.cpp:394:92: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:05:16,862 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2023-09-12T11:05:16,862 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:05:16,863 ./src/formats/mol2format.cpp:476:99: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:05:16,864 476 | if (n_h_bonded < min_n_h_bonded || (n_h_bonded == min_n_h_bonded && partner->GetIdx() < min_idx)) { 2023-09-12T11:05:16,865 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:05:16,865 ./src/formats/mol2format.cpp:499:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:05:16,865 499 | if (partner->GetIdx() == min_idx) { 2023-09-12T11:05:16,866 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:05:16,894 ./src/formats/mol2format.cpp: In member function ‘virtual int OpenBabel::MOL2Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:05:16,895 ./src/formats/mol2format.cpp:727:10: warning: unused variable ‘ch’ [-Wunused-variable] 2023-09-12T11:05:16,895 727 | char ch = ifs.peek(); 2023-09-12T11:05:16,896 | ^~ 2023-09-12T11:05:22,517 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:22,517 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/ccHSZ5d6.s 2023-09-12T11:05:22,522 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:22,909 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/ 2023-09-12T11:05:22,910 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/ 2023-09-12T11:05:22,910 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:05:22,912 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 2023-09-12T11:05:22,916 Using built-in specs. 2023-09-12T11:05:22,916 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:22,917 Target: arm-linux-gnueabihf 2023-09-12T11:05:22,918 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 2023-09-12T11:05:22,918 Thread model: posix 2023-09-12T11:05:22,919 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:22,919 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:22,920 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:22,920 /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/ccmNZeS1.s 2023-09-12T11:05:22,929 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:22,930 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 2023-09-12T11:05:22,931 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:22,931 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:22,932 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:22,932 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:22,933 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:22,933 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:22,934 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:22,934 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:22,935 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:22,936 #include "..." search starts here: 2023-09-12T11:05:22,936 #include <...> search starts here: 2023-09-12T11:05:22,937 /usr/include/eigen3 2023-09-12T11:05:22,937 include 2023-09-12T11:05:22,938 /usr/include/python3.11 2023-09-12T11:05:22,939 /usr/include/c++/12 2023-09-12T11:05:22,939 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:22,940 /usr/include/c++/12/backward 2023-09-12T11:05:22,941 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:22,941 /usr/local/include 2023-09-12T11:05:22,942 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:22,943 /usr/include 2023-09-12T11:05:22,943 End of search list. 2023-09-12T11:05:22,944 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:22,944 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 2023-09-12T11:05:22,945 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:22,945 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:22,947 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:24,478 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:24,479 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:24,480 from ./src/formats/moldenformat.cpp:35: 2023-09-12T11:05:24,480 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:24,481 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:24,481 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:24,482 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:05:24,482 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:05:24,483 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:05:24,483 from /usr/include/c++/12/ios:42, 2023-09-12T11:05:24,484 from /usr/include/c++/12/istream:38, 2023-09-12T11:05:24,485 from /usr/include/c++/12/fstream:38, 2023-09-12T11:05:24,485 from ./src/formats/moldenformat.cpp:27: 2023-09-12T11:05:24,486 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:24,487 131 | struct binary_function 2023-09-12T11:05:24,487 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:24,705 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:24,706 from include/openbabel/mol.h:43, 2023-09-12T11:05:24,707 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:24,708 from ./src/formats/moldenformat.cpp:36: 2023-09-12T11:05:24,708 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:24,709 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:24,710 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:24,711 | ^ 2023-09-12T11:05:24,711 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:24,712 37 | # define UNUSED(x) x 2023-09-12T11:05:24,713 | ^ 2023-09-12T11:05:25,376 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:25,376 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:25,377 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:25,378 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:25,378 | ^ 2023-09-12T11:05:25,379 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:25,380 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:25,381 | ^~~~~~~~ 2023-09-12T11:05:25,382 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:25,382 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:25,383 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:25,383 | ^ 2023-09-12T11:05:25,384 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:25,384 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:25,385 | ^~~~~~~~ 2023-09-12T11:05:25,401 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:25,402 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:25,403 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:25,403 | ^ 2023-09-12T11:05:25,404 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:25,404 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:25,405 | ^~~~~~~~ 2023-09-12T11:05:25,408 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:25,408 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:25,409 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:25,410 | ^ 2023-09-12T11:05:25,411 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:25,411 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:25,412 | ^~~~~~~~ 2023-09-12T11:05:25,658 ./src/formats/moldenformat.cpp: In member function ‘virtual int OpenBabel::OBMoldenFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:05:25,659 ./src/formats/moldenformat.cpp:85:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:05:25,659 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:05:25,660 | ~~~~^ 2023-09-12T11:05:25,661 ./src/formats/moldenformat.cpp:85:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:05:25,661 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:05:25,662 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:05:25,671 ./src/formats/moldenformat.cpp: In member function ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:25,672 ./src/formats/moldenformat.cpp:171:48: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:05:25,673 171 | if (sscanf(lineBuffer.c_str(), "%d", &natoms) == 0 || !natoms) { 2023-09-12T11:05:25,674 | ~^ ~~~~~~~ 2023-09-12T11:05:25,674 | | | 2023-09-12T11:05:25,675 | | unsigned int* 2023-09-12T11:05:25,675 | int* 2023-09-12T11:05:25,676 | %d 2023-09-12T11:05:28,820 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:05:28,820 from ./src/formats/moldenformat.cpp:29: 2023-09-12T11:05:28,821 /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]’: 2023-09-12T11:05:28,821 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:28,822 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:05:28,822 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:28,880 /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]’: 2023-09-12T11:05:28,880 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:28,950 /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]’: 2023-09-12T11:05:28,951 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:30,473 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:05:30,473 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:30,474 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:192:33: 2023-09-12T11:05:30,475 /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 2023-09-12T11:05:30,476 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:30,476 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:30,477 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:05:30,478 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:208:38: 2023-09-12T11:05:30,478 /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 2023-09-12T11:05:30,479 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:30,480 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:30,480 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:30,481 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:240:36: 2023-09-12T11:05:30,482 /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 2023-09-12T11:05:30,483 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:30,484 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:30,484 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:30,485 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:251:36: 2023-09-12T11:05:30,485 /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 2023-09-12T11:05:30,486 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:30,486 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:30,487 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:05:30,487 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, 2023-09-12T11:05:30,488 inlined from ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/moldenformat.cpp:290:32: 2023-09-12T11:05:30,488 /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 2023-09-12T11:05:30,489 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:30,490 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:32,671 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:32,672 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/ccmNZeS1.s 2023-09-12T11:05:32,676 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:33,192 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/ 2023-09-12T11:05:33,193 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/ 2023-09-12T11:05:33,193 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/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.' 2023-09-12T11:05:33,197 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 2023-09-12T11:05:33,201 Using built-in specs. 2023-09-12T11:05:33,201 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:33,202 Target: arm-linux-gnueabihf 2023-09-12T11:05:33,202 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 2023-09-12T11:05:33,203 Thread model: posix 2023-09-12T11:05:33,203 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:33,204 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:33,204 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:33,205 /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/ccLtTphz.s 2023-09-12T11:05:33,214 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:33,214 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:33,215 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:33,216 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:33,217 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:33,217 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:33,218 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:33,218 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:33,219 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:33,220 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:33,221 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:33,221 #include "..." search starts here: 2023-09-12T11:05:33,222 #include <...> search starts here: 2023-09-12T11:05:33,222 /usr/include/eigen3 2023-09-12T11:05:33,222 include 2023-09-12T11:05:33,223 /usr/include/python3.11 2023-09-12T11:05:33,223 /usr/include/c++/12 2023-09-12T11:05:33,224 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:33,224 /usr/include/c++/12/backward 2023-09-12T11:05:33,224 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:33,225 /usr/local/include 2023-09-12T11:05:33,225 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:33,226 /usr/include 2023-09-12T11:05:33,226 End of search list. 2023-09-12T11:05:33,227 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:33,227 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:33,228 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:33,228 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:33,234 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:34,826 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:34,827 from include/openbabel/mol.h:43, 2023-09-12T11:05:34,828 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:34,828 from ./src/formats/molproformat.cpp:20: 2023-09-12T11:05:34,829 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:34,829 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:34,830 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:34,831 | ^ 2023-09-12T11:05:34,831 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:34,832 37 | # define UNUSED(x) x 2023-09-12T11:05:34,833 | ^ 2023-09-12T11:05:35,593 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:35,594 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:35,595 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:35,596 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:35,596 | ^ 2023-09-12T11:05:35,597 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:35,598 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:35,598 | ^~~~~~~~ 2023-09-12T11:05:35,599 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:35,600 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:35,601 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:35,601 | ^ 2023-09-12T11:05:35,602 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:35,603 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:35,604 | ^~~~~~~~ 2023-09-12T11:05:35,619 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:35,619 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:35,620 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:35,621 | ^ 2023-09-12T11:05:35,621 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:35,622 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:35,622 | ^~~~~~~~ 2023-09-12T11:05:35,626 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:35,626 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:35,627 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:35,627 | ^ 2023-09-12T11:05:35,628 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:35,628 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:35,629 | ^~~~~~~~ 2023-09-12T11:05:35,801 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:35,802 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:35,802 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:35,803 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:35,804 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:35,805 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:35,805 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:35,806 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:35,807 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:35,807 from include/openbabel/mol.h:35: 2023-09-12T11:05:35,808 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:35,809 131 | struct binary_function 2023-09-12T11:05:35,809 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:39,116 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:05:39,117 /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]’: 2023-09-12T11:05:39,117 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:39,118 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:05:39,119 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:39,167 /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]’: 2023-09-12T11:05:39,168 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:39,356 /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]’: 2023-09-12T11:05:39,356 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:39,989 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:39,990 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, 2023-09-12T11:05:39,991 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:189:33: 2023-09-12T11:05:39,991 /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 2023-09-12T11:05:39,992 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:39,992 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:39,993 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:39,994 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, 2023-09-12T11:05:39,994 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:191:33: 2023-09-12T11:05:39,995 /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 2023-09-12T11:05:39,996 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:39,997 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:39,997 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:39,998 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, 2023-09-12T11:05:39,999 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:198:33: 2023-09-12T11:05:39,999 /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 2023-09-12T11:05:40,000 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:40,001 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:40,001 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:40,002 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, 2023-09-12T11:05:40,003 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:206:28: 2023-09-12T11:05:40,003 /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 2023-09-12T11:05:40,004 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:40,005 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:40,005 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:40,006 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, 2023-09-12T11:05:40,006 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:210:28: 2023-09-12T11:05:40,007 /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 2023-09-12T11:05:40,007 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:40,008 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:40,008 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:40,009 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, 2023-09-12T11:05:40,010 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:214:28: 2023-09-12T11:05:40,010 /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 2023-09-12T11:05:40,011 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:40,012 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:40,013 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:05:40,013 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, 2023-09-12T11:05:40,014 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:217:33: 2023-09-12T11:05:40,015 /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 2023-09-12T11:05:40,015 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:40,016 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:40,017 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:05:40,017 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:40,018 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:223:29: 2023-09-12T11:05:40,019 /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 2023-09-12T11:05:40,020 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:40,021 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:40,021 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:40,021 inlined from ‘virtual bool OpenBabel::MolproOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/molproformat.cpp:224:36: 2023-09-12T11:05:40,022 /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 2023-09-12T11:05:40,023 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:05:40,023 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:05:41,263 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:41,264 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/ccLtTphz.s 2023-09-12T11:05:41,268 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:41,652 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/ 2023-09-12T11:05:41,652 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/ 2023-09-12T11:05:41,653 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:05:41,655 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 2023-09-12T11:05:41,658 Using built-in specs. 2023-09-12T11:05:41,659 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:41,660 Target: arm-linux-gnueabihf 2023-09-12T11:05:41,660 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 2023-09-12T11:05:41,661 Thread model: posix 2023-09-12T11:05:41,662 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:41,662 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:41,663 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:41,664 /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/ccdHo1xQ.s 2023-09-12T11:05:41,672 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:41,672 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:41,674 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:41,674 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:41,675 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:41,675 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:41,676 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:41,677 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:41,678 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:41,678 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:41,679 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:41,679 #include "..." search starts here: 2023-09-12T11:05:41,680 #include <...> search starts here: 2023-09-12T11:05:41,680 /usr/include/eigen3 2023-09-12T11:05:41,681 include 2023-09-12T11:05:41,681 /usr/include/python3.11 2023-09-12T11:05:41,682 /usr/include/c++/12 2023-09-12T11:05:41,683 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:41,683 /usr/include/c++/12/backward 2023-09-12T11:05:41,684 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:41,684 /usr/local/include 2023-09-12T11:05:41,685 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:41,686 /usr/include 2023-09-12T11:05:41,686 End of search list. 2023-09-12T11:05:41,687 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:41,688 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:41,689 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:41,690 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:41,694 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:43,254 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:43,254 from include/openbabel/mol.h:43, 2023-09-12T11:05:43,255 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:43,255 from ./src/formats/molreport.cpp:21: 2023-09-12T11:05:43,256 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:43,256 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:43,257 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:43,257 | ^ 2023-09-12T11:05:43,258 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:43,258 37 | # define UNUSED(x) x 2023-09-12T11:05:43,259 | ^ 2023-09-12T11:05:44,022 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:44,022 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:44,023 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:44,024 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:44,024 | ^ 2023-09-12T11:05:44,025 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:44,026 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:44,027 | ^~~~~~~~ 2023-09-12T11:05:44,028 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:44,029 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:44,030 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:44,031 | ^ 2023-09-12T11:05:44,032 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:44,032 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:44,033 | ^~~~~~~~ 2023-09-12T11:05:44,048 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:44,049 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:44,050 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:44,050 | ^ 2023-09-12T11:05:44,051 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:44,052 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:44,053 | ^~~~~~~~ 2023-09-12T11:05:44,056 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:44,057 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:44,057 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:44,058 | ^ 2023-09-12T11:05:44,058 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:44,059 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:44,060 | ^~~~~~~~ 2023-09-12T11:05:44,230 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:44,230 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:44,231 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:44,231 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:44,232 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:44,233 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:44,233 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:44,234 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:44,235 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:44,235 from include/openbabel/mol.h:35: 2023-09-12T11:05:44,236 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:44,237 131 | struct binary_function 2023-09-12T11:05:44,237 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:46,649 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:46,649 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/ccdHo1xQ.s 2023-09-12T11:05:46,654 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:46,795 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/ 2023-09-12T11:05:46,796 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/ 2023-09-12T11:05:46,796 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:05:46,797 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 2023-09-12T11:05:46,801 Using built-in specs. 2023-09-12T11:05:46,802 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:46,802 Target: arm-linux-gnueabihf 2023-09-12T11:05:46,803 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 2023-09-12T11:05:46,803 Thread model: posix 2023-09-12T11:05:46,804 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:46,805 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:46,805 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:05:46,806 /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/cc7dJn3F.s 2023-09-12T11:05:46,814 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:46,815 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:46,816 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:46,817 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:46,817 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:46,818 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:46,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:46,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:46,820 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:46,821 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:46,821 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:46,822 #include "..." search starts here: 2023-09-12T11:05:46,822 #include <...> search starts here: 2023-09-12T11:05:46,822 /usr/include/eigen3 2023-09-12T11:05:46,823 include 2023-09-12T11:05:46,823 /usr/include/python3.11 2023-09-12T11:05:46,824 /usr/include/c++/12 2023-09-12T11:05:46,824 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:46,825 /usr/include/c++/12/backward 2023-09-12T11:05:46,825 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:46,826 /usr/local/include 2023-09-12T11:05:46,826 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:46,826 /usr/include 2023-09-12T11:05:46,827 End of search list. 2023-09-12T11:05:46,828 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:46,828 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:46,829 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:46,829 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:46,832 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:05:48,391 In file included from include/openbabel/atom.h:33, 2023-09-12T11:05:48,392 from include/openbabel/mol.h:43, 2023-09-12T11:05:48,393 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:05:48,394 from ./src/formats/mopacformat.cpp:17: 2023-09-12T11:05:48,394 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:05:48,395 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:05:48,396 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:05:48,396 | ^ 2023-09-12T11:05:48,397 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:05:48,398 37 | # define UNUSED(x) x 2023-09-12T11:05:48,399 | ^ 2023-09-12T11:05:49,160 In file included from include/openbabel/mol.h:52: 2023-09-12T11:05:49,161 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:49,161 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:49,162 862 | {return new OBVibrationData(*this);} 2023-09-12T11:05:49,163 | ^ 2023-09-12T11:05:49,164 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:05:49,164 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:05:49,165 | ^~~~~~~~ 2023-09-12T11:05:49,166 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:49,167 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:49,167 907 | {return new OBDOSData(*this);} 2023-09-12T11:05:49,168 | ^ 2023-09-12T11:05:49,169 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:05:49,170 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:05:49,170 | ^~~~~~~~ 2023-09-12T11:05:49,184 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:49,185 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:49,185 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:05:49,186 | ^ 2023-09-12T11:05:49,186 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:05:49,187 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:05:49,188 | ^~~~~~~~ 2023-09-12T11:05:49,190 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:05:49,191 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:05:49,192 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:05:49,192 | ^ 2023-09-12T11:05:49,193 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:05:49,194 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:05:49,195 | ^~~~~~~~ 2023-09-12T11:05:49,363 In file included from include/openbabel/format.h:22, 2023-09-12T11:05:49,364 from include/openbabel/obconversion.h:37, 2023-09-12T11:05:49,364 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:05:49,365 include/openbabel/plugin.h: At global scope: 2023-09-12T11:05:49,366 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:05:49,367 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:05:49,367 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:49,368 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:05:49,369 from /usr/include/c++/12/vector:66, 2023-09-12T11:05:49,369 from include/openbabel/mol.h:35: 2023-09-12T11:05:49,370 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:05:49,371 131 | struct binary_function 2023-09-12T11:05:49,371 | ^~~~~~~~~~~~~~~ 2023-09-12T11:05:49,626 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACCARTFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:49,627 ./src/formats/mopacformat.cpp:642:19: warning: variable ‘isotopeMass’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:05:49,627 642 | double x,y,z, isotopeMass; 2023-09-12T11:05:49,628 | ^~~~~~~~~~~ 2023-09-12T11:05:54,587 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:05:54,588 /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]’: 2023-09-12T11:05:54,589 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:54,590 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:05:54,590 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:54,648 /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]’: 2023-09-12T11:05:54,649 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:05:55,828 In file included from include/openbabel/atom.h:35: 2023-09-12T11:05:55,828 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2023-09-12T11:05:55,829 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2023-09-12T11:05:55,829 include/openbabel/math/vector3.h:91:11: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:55,830 91 | _vy = inY; 2023-09-12T11:05:55,830 | ~~~~^~~~~ 2023-09-12T11:05:55,831 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:55,832 ./src/formats/mopacformat.cpp:73:14: note: ‘y’ was declared here 2023-09-12T11:05:55,832 73 | double x,y,z; 2023-09-12T11:05:55,833 | ^ 2023-09-12T11:05:55,834 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2023-09-12T11:05:55,835 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2023-09-12T11:05:55,836 include/openbabel/math/vector3.h:90:11: warning: ‘x’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:05:55,836 90 | _vx = inX; 2023-09-12T11:05:55,837 | ~~~~^~~~~ 2023-09-12T11:05:55,838 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:05:55,839 ./src/formats/mopacformat.cpp:73:12: note: ‘x’ was declared here 2023-09-12T11:05:55,840 73 | double x,y,z; 2023-09-12T11:05:55,841 | ^ 2023-09-12T11:05:55,884 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,884 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, 2023-09-12T11:05:55,885 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:283:42: 2023-09-12T11:05:55,886 /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 2023-09-12T11:05:55,886 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,887 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,888 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,889 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, 2023-09-12T11:05:55,889 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:309:34: 2023-09-12T11:05:55,890 /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 2023-09-12T11:05:55,891 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,891 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,892 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,893 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, 2023-09-12T11:05:55,893 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:331:34: 2023-09-12T11:05:55,894 /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 2023-09-12T11:05:55,894 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,895 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,895 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,896 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, 2023-09-12T11:05:55,897 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:377:36: 2023-09-12T11:05:55,898 /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 2023-09-12T11:05:55,898 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,899 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,900 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,901 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, 2023-09-12T11:05:55,902 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:396:28: 2023-09-12T11:05:55,902 /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 2023-09-12T11:05:55,903 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,904 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,904 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,905 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, 2023-09-12T11:05:55,906 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:402:28: 2023-09-12T11:05:55,907 /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 2023-09-12T11:05:55,908 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,908 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,909 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,909 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, 2023-09-12T11:05:55,910 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:409:28: 2023-09-12T11:05:55,910 /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 2023-09-12T11:05:55,911 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,911 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,912 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:05:55,912 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, 2023-09-12T11:05:55,913 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:416:59: 2023-09-12T11:05:55,913 /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 2023-09-12T11:05:55,914 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,915 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:55,916 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:05:55,916 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, 2023-09-12T11:05:55,917 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:433:34: 2023-09-12T11:05:55,918 /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 2023-09-12T11:05:55,919 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:05:55,920 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:05:58,751 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/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/' 2023-09-12T11:05:58,752 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/cc7dJn3F.s 2023-09-12T11:05:58,756 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:05:59,412 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/ 2023-09-12T11:05:59,412 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/ 2023-09-12T11:05:59,413 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/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.' 2023-09-12T11:05:59,416 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 2023-09-12T11:05:59,420 Using built-in specs. 2023-09-12T11:05:59,420 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:05:59,421 Target: arm-linux-gnueabihf 2023-09-12T11:05:59,422 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 2023-09-12T11:05:59,422 Thread model: posix 2023-09-12T11:05:59,423 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:05:59,423 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:05:59,424 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/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/' 2023-09-12T11:05:59,424 /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/ccTePFUE.s 2023-09-12T11:05:59,433 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:59,434 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:59,435 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:59,435 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:59,436 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:05:59,436 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:05:59,436 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:05:59,437 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:05:59,437 ignoring duplicate directory "/usr/include/" 2023-09-12T11:05:59,438 as it is a non-system directory that duplicates a system directory 2023-09-12T11:05:59,438 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:05:59,439 #include "..." search starts here: 2023-09-12T11:05:59,439 #include <...> search starts here: 2023-09-12T11:05:59,440 /usr/include/eigen3 2023-09-12T11:05:59,440 include 2023-09-12T11:05:59,441 /usr/include/python3.11 2023-09-12T11:05:59,441 /usr/include/c++/12 2023-09-12T11:05:59,442 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:05:59,443 /usr/include/c++/12/backward 2023-09-12T11:05:59,443 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:05:59,444 /usr/local/include 2023-09-12T11:05:59,444 /usr/include/arm-linux-gnueabihf 2023-09-12T11:05:59,445 /usr/include 2023-09-12T11:05:59,445 End of search list. 2023-09-12T11:05:59,446 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:05:59,447 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:05:59,448 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:05:59,449 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:05:59,451 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:01,007 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:01,008 from include/openbabel/mol.h:43, 2023-09-12T11:06:01,008 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:01,009 from ./src/formats/mpdformat.cpp:22: 2023-09-12T11:06:01,010 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:01,010 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:01,011 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:01,011 | ^ 2023-09-12T11:06:01,012 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:01,013 37 | # define UNUSED(x) x 2023-09-12T11:06:01,013 | ^ 2023-09-12T11:06:01,774 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:01,775 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:01,776 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:01,777 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:01,777 | ^ 2023-09-12T11:06:01,778 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:01,778 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:01,779 | ^~~~~~~~ 2023-09-12T11:06:01,780 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:01,780 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:01,781 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:01,781 | ^ 2023-09-12T11:06:01,782 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:01,782 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:01,783 | ^~~~~~~~ 2023-09-12T11:06:01,798 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:01,799 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:01,800 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:01,800 | ^ 2023-09-12T11:06:01,801 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:01,802 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:01,803 | ^~~~~~~~ 2023-09-12T11:06:01,805 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:01,805 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:01,806 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:01,807 | ^ 2023-09-12T11:06:01,808 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:01,808 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:01,809 | ^~~~~~~~ 2023-09-12T11:06:01,978 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:01,978 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:01,979 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:01,980 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:01,981 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:01,981 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:01,982 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:01,983 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:01,984 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:01,984 from include/openbabel/mol.h:35: 2023-09-12T11:06:01,985 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:01,985 131 | struct binary_function 2023-09-12T11:06:01,985 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:02,201 ./src/formats/mpdformat.cpp: In member function ‘virtual bool OpenBabel::MPDFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:02,202 ./src/formats/mpdformat.cpp:204:42: warning: variable ‘idx_true’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:06:02,202 204 | bool xml_true=false, pre_true=false, idx_true=false; 2023-09-12T11:06:02,203 | ^~~~~~~~ 2023-09-12T11:06:04,846 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:06:04,847 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/mpdformat.o /tmp/ccTePFUE.s 2023-09-12T11:06:04,852 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:05,030 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/ 2023-09-12T11:06:05,031 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/ 2023-09-12T11:06:05,032 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:06:05,034 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 2023-09-12T11:06:05,037 Using built-in specs. 2023-09-12T11:06:05,038 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:05,039 Target: arm-linux-gnueabihf 2023-09-12T11:06:05,039 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 2023-09-12T11:06:05,040 Thread model: posix 2023-09-12T11:06:05,041 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:05,041 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:05,042 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:06:05,042 /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/ccZQ1Yj7.s 2023-09-12T11:06:05,051 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:05,052 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:05,053 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:05,053 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:05,054 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:05,055 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:05,055 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:05,056 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:05,056 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:05,057 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:05,057 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:05,058 #include "..." search starts here: 2023-09-12T11:06:05,058 #include <...> search starts here: 2023-09-12T11:06:05,059 /usr/include/eigen3 2023-09-12T11:06:05,060 include 2023-09-12T11:06:05,060 /usr/include/python3.11 2023-09-12T11:06:05,061 /usr/include/c++/12 2023-09-12T11:06:05,062 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:05,062 /usr/include/c++/12/backward 2023-09-12T11:06:05,063 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:05,063 /usr/local/include 2023-09-12T11:06:05,064 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:05,065 /usr/include 2023-09-12T11:06:05,065 End of search list. 2023-09-12T11:06:05,066 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:05,067 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 2023-09-12T11:06:05,068 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:05,069 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:05,071 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:06,640 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:06,641 from include/openbabel/mol.h:43, 2023-09-12T11:06:06,641 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:06,642 from ./src/formats/mpqcformat.cpp:16: 2023-09-12T11:06:06,643 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:06,643 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:06,644 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:06,644 | ^ 2023-09-12T11:06:06,645 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:06,645 37 | # define UNUSED(x) x 2023-09-12T11:06:06,646 | ^ 2023-09-12T11:06:07,417 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:07,418 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,418 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,419 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:07,420 | ^ 2023-09-12T11:06:07,421 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:07,421 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:07,422 | ^~~~~~~~ 2023-09-12T11:06:07,423 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,424 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,424 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:07,425 | ^ 2023-09-12T11:06:07,426 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:07,426 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:07,427 | ^~~~~~~~ 2023-09-12T11:06:07,442 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,443 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,444 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:07,444 | ^ 2023-09-12T11:06:07,445 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:07,446 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:07,447 | ^~~~~~~~ 2023-09-12T11:06:07,449 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:07,450 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:07,450 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:07,451 | ^ 2023-09-12T11:06:07,451 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:07,452 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:07,452 | ^~~~~~~~ 2023-09-12T11:06:07,622 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:07,622 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:07,623 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:07,624 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:07,624 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:07,625 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:07,625 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:07,626 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:07,627 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:07,628 from include/openbabel/mol.h:35: 2023-09-12T11:06:07,628 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:07,629 131 | struct binary_function 2023-09-12T11:06:07,630 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:10,317 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:06:10,318 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/ccZQ1Yj7.s 2023-09-12T11:06:10,326 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:10,487 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/ 2023-09-12T11:06:10,488 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/ 2023-09-12T11:06:10,489 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:06:10,489 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/msiformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/msiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:10,494 Using built-in specs. 2023-09-12T11:06:10,495 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:10,495 Target: arm-linux-gnueabihf 2023-09-12T11:06:10,496 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 2023-09-12T11:06:10,496 Thread model: posix 2023-09-12T11:06:10,497 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:10,497 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:10,498 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/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/' 2023-09-12T11:06:10,498 /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/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/ccEl7QQK.s 2023-09-12T11:06:10,508 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:10,508 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:10,509 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:10,510 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:10,511 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:10,511 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:10,512 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:10,513 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:10,513 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:10,514 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:10,514 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:10,515 #include "..." search starts here: 2023-09-12T11:06:10,515 #include <...> search starts here: 2023-09-12T11:06:10,515 /usr/include/eigen3 2023-09-12T11:06:10,516 include 2023-09-12T11:06:10,516 /usr/include/python3.11 2023-09-12T11:06:10,517 /usr/include/c++/12 2023-09-12T11:06:10,517 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:10,517 /usr/include/c++/12/backward 2023-09-12T11:06:10,518 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:10,518 /usr/local/include 2023-09-12T11:06:10,519 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:10,519 /usr/include 2023-09-12T11:06:10,520 End of search list. 2023-09-12T11:06:10,520 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:10,521 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:10,522 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:10,522 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:10,528 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:12,093 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:12,094 from include/openbabel/mol.h:43, 2023-09-12T11:06:12,095 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:12,095 from ./src/formats/msiformat.cpp:15: 2023-09-12T11:06:12,096 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:12,097 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:12,098 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:12,098 | ^ 2023-09-12T11:06:12,099 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:12,100 37 | # define UNUSED(x) x 2023-09-12T11:06:12,101 | ^ 2023-09-12T11:06:12,863 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:12,863 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:12,864 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:12,864 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:12,865 | ^ 2023-09-12T11:06:12,866 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:12,866 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:12,867 | ^~~~~~~~ 2023-09-12T11:06:12,868 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:12,869 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:12,870 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:12,871 | ^ 2023-09-12T11:06:12,871 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:12,872 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:12,872 | ^~~~~~~~ 2023-09-12T11:06:12,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:12,889 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:12,890 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:12,890 | ^ 2023-09-12T11:06:12,891 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:12,892 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:12,892 | ^~~~~~~~ 2023-09-12T11:06:12,896 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:12,896 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:12,897 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:12,898 | ^ 2023-09-12T11:06:12,899 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:12,899 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:12,900 | ^~~~~~~~ 2023-09-12T11:06:13,070 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:13,071 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:13,071 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:13,072 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:13,073 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:13,074 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:13,074 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:13,075 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:13,076 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:13,076 from include/openbabel/mol.h:35: 2023-09-12T11:06:13,077 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:13,078 131 | struct binary_function 2023-09-12T11:06:13,078 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:13,286 ./src/formats/msiformat.cpp: In member function ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:13,287 ./src/formats/msiformat.cpp:71:17: warning: unused variable ‘title’ [-Wunused-variable] 2023-09-12T11:06:13,287 71 | const char* title = pConv->GetTitle(); 2023-09-12T11:06:13,288 | ^~~~~ 2023-09-12T11:06:15,700 In member function ‘void OpenBabel::OBUnitCell::SetSpaceGroup(const OpenBabel::SpaceGroup*)’, 2023-09-12T11:06:15,701 inlined from ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/msiformat.cpp:265:26: 2023-09-12T11:06:15,701 include/openbabel/generic.h:366:60: warning: ‘sg’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:15,702 366 | void SetSpaceGroup(const SpaceGroup* sg) { _spaceGroup = sg; } 2023-09-12T11:06:15,702 | ~~~~~~~~~~~~^~~~ 2023-09-12T11:06:15,703 ./src/formats/msiformat.cpp: In member function ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:15,704 ./src/formats/msiformat.cpp:106:23: note: ‘sg’ was declared here 2023-09-12T11:06:15,704 106 | const SpaceGroup *sg; 2023-09-12T11:06:15,705 | ^~ 2023-09-12T11:06:15,705 ./src/formats/msiformat.cpp:189:28: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:15,706 189 | atom->SetVector(atof(vs[3].c_str()), 2023-09-12T11:06:15,707 | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:15,707 190 | atof(vs[4].c_str()), 2023-09-12T11:06:15,708 | ~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:15,708 191 | atof(vs[5].c_str())); 2023-09-12T11:06:15,709 | ~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:15,710 ./src/formats/msiformat.cpp:103:13: note: ‘atom’ was declared here 2023-09-12T11:06:15,710 103 | OBAtom *atom; 2023-09-12T11:06:15,711 | ^~~~ 2023-09-12T11:06:15,712 ./src/formats/msiformat.cpp:235:24: warning: ‘bondOrder’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:15,712 235 | mol.AddBond(startBondAtom - 1, endBondAtom - 1, bondOrder); 2023-09-12T11:06:15,713 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:15,714 ./src/formats/msiformat.cpp:100:46: note: ‘bondOrder’ was declared here 2023-09-12T11:06:15,715 100 | unsigned int startBondAtom, endBondAtom, bondOrder; 2023-09-12T11:06:15,715 | ^~~~~~~~~ 2023-09-12T11:06:15,716 ./src/formats/msiformat.cpp:235:56: warning: ‘endBondAtom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:15,717 235 | mol.AddBond(startBondAtom - 1, endBondAtom - 1, bondOrder); 2023-09-12T11:06:15,718 | ~~~~~~~~~~~~^~~ 2023-09-12T11:06:15,718 ./src/formats/msiformat.cpp:100:33: note: ‘endBondAtom’ was declared here 2023-09-12T11:06:15,719 100 | unsigned int startBondAtom, endBondAtom, bondOrder; 2023-09-12T11:06:15,720 | ^~~~~~~~~~~ 2023-09-12T11:06:15,720 ./src/formats/msiformat.cpp:235:39: warning: ‘startBondAtom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:15,721 235 | mol.AddBond(startBondAtom - 1, endBondAtom - 1, bondOrder); 2023-09-12T11:06:15,722 | ~~~~~~~~~~~~~~^~~ 2023-09-12T11:06:15,722 ./src/formats/msiformat.cpp:100:18: note: ‘startBondAtom’ was declared here 2023-09-12T11:06:15,723 100 | unsigned int startBondAtom, endBondAtom, bondOrder; 2023-09-12T11:06:15,724 | ^~~~~~~~~~~~~ 2023-09-12T11:06:16,334 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:06:16,335 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/ccEl7QQK.s 2023-09-12T11:06:16,340 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:16,547 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/ 2023-09-12T11:06:16,548 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/ 2023-09-12T11:06:16,548 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/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.' 2023-09-12T11:06:16,549 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/msmsformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/msmsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:16,553 Using built-in specs. 2023-09-12T11:06:16,554 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:16,555 Target: arm-linux-gnueabihf 2023-09-12T11:06:16,555 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 2023-09-12T11:06:16,556 Thread model: posix 2023-09-12T11:06:16,557 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:16,557 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:16,558 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/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/' 2023-09-12T11:06:16,558 /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/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/ccv2bSZr.s 2023-09-12T11:06:16,568 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:16,569 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:16,570 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:16,570 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:16,571 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:16,571 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:16,572 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:16,572 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:16,573 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:16,573 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:16,574 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:16,574 #include "..." search starts here: 2023-09-12T11:06:16,575 #include <...> search starts here: 2023-09-12T11:06:16,575 /usr/include/eigen3 2023-09-12T11:06:16,576 include 2023-09-12T11:06:16,577 /usr/include/python3.11 2023-09-12T11:06:16,577 /usr/include/c++/12 2023-09-12T11:06:16,578 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:16,579 /usr/include/c++/12/backward 2023-09-12T11:06:16,579 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:16,580 /usr/local/include 2023-09-12T11:06:16,581 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:16,581 /usr/include 2023-09-12T11:06:16,582 End of search list. 2023-09-12T11:06:16,582 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:16,583 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:16,585 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:16,585 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:16,590 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:18,156 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:18,157 from include/openbabel/mol.h:43, 2023-09-12T11:06:18,157 from ./src/formats/msmsformat.cpp:26: 2023-09-12T11:06:18,158 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:18,159 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:18,159 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:18,160 | ^ 2023-09-12T11:06:18,161 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:18,161 37 | # define UNUSED(x) x 2023-09-12T11:06:18,162 | ^ 2023-09-12T11:06:19,921 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:19,976 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:20,066 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:20,122 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:20,123 | ^ 2023-09-12T11:06:20,132 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:20,133 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:20,144 | ^~~~~~~~ 2023-09-12T11:06:20,176 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:20,180 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:20,182 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:20,192 | ^ 2023-09-12T11:06:20,196 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:20,235 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:20,240 | ^~~~~~~~ 2023-09-12T11:06:20,248 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:20,298 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:20,338 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:20,344 | ^ 2023-09-12T11:06:20,353 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:20,364 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:20,365 | ^~~~~~~~ 2023-09-12T11:06:20,376 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:20,427 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:20,507 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:20,508 | ^ 2023-09-12T11:06:20,509 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:20,509 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:20,510 | ^~~~~~~~ 2023-09-12T11:06:20,511 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:20,512 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:20,513 from ./src/formats/msmsformat.cpp:27: 2023-09-12T11:06:20,514 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:20,515 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:20,516 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:20,517 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:20,517 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:20,518 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:20,519 from include/openbabel/mol.h:35: 2023-09-12T11:06:20,519 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:20,520 131 | struct binary_function 2023-09-12T11:06:20,520 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:20,521 ./src/formats/msmsformat.cpp: In member function ‘virtual int OpenBabel::OBMSMSFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:06:20,522 ./src/formats/msmsformat.cpp:82:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:06:20,522 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:06:20,523 | ~~~~^ 2023-09-12T11:06:20,524 ./src/formats/msmsformat.cpp:82:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:06:20,524 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:06:20,525 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:06:22,678 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/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/' 2023-09-12T11:06:22,679 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/ccv2bSZr.s 2023-09-12T11:06:22,683 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:23,023 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/ 2023-09-12T11:06:23,024 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/ 2023-09-12T11:06:23,025 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:06:23,025 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 2023-09-12T11:06:23,030 Using built-in specs. 2023-09-12T11:06:23,031 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:23,031 Target: arm-linux-gnueabihf 2023-09-12T11:06:23,032 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 2023-09-12T11:06:23,032 Thread model: posix 2023-09-12T11:06:23,033 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:23,033 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:23,034 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:06:23,034 /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/ccGfVAQR.s 2023-09-12T11:06:23,044 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:23,044 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:23,046 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:23,047 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:23,047 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:23,048 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:23,048 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:23,049 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:23,050 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:23,050 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:23,051 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:23,052 #include "..." search starts here: 2023-09-12T11:06:23,052 #include <...> search starts here: 2023-09-12T11:06:23,053 /usr/include/eigen3 2023-09-12T11:06:23,054 include 2023-09-12T11:06:23,055 /usr/include/python3.11 2023-09-12T11:06:23,055 /usr/include/c++/12 2023-09-12T11:06:23,056 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:23,057 /usr/include/c++/12/backward 2023-09-12T11:06:23,058 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:23,058 /usr/local/include 2023-09-12T11:06:23,059 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:23,059 /usr/include 2023-09-12T11:06:23,060 End of search list. 2023-09-12T11:06:23,060 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:23,061 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:23,062 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:23,062 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:23,063 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:24,951 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:24,952 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:24,952 from ./src/formats/nulformat.cpp:14: 2023-09-12T11:06:24,953 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:24,953 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:24,954 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:24,955 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:06:24,955 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:06:24,956 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:06:24,956 from /usr/include/c++/12/ios:42, 2023-09-12T11:06:24,957 from /usr/include/c++/12/ostream:38, 2023-09-12T11:06:24,958 from /usr/include/c++/12/iostream:39, 2023-09-12T11:06:24,959 from include/openbabel/obconversion.h:24: 2023-09-12T11:06:24,959 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:24,960 131 | struct binary_function 2023-09-12T11:06:24,961 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:25,116 In file included from ./src/formats/nulformat.cpp:15: 2023-09-12T11:06:25,117 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:25,118 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:25,119 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:25,120 | ^ 2023-09-12T11:06:25,120 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:25,121 37 | # define UNUSED(x) x 2023-09-12T11:06:25,122 | ^ 2023-09-12T11:06:25,990 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/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/' 2023-09-12T11:06:25,991 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/ccGfVAQR.s 2023-09-12T11:06:25,996 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:26,072 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/ 2023-09-12T11:06:26,073 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/ 2023-09-12T11:06:26,074 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/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.' 2023-09-12T11:06:26,074 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/nwchemformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/nwchemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:26,078 Using built-in specs. 2023-09-12T11:06:26,079 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:26,080 Target: arm-linux-gnueabihf 2023-09-12T11:06:26,080 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 2023-09-12T11:06:26,081 Thread model: posix 2023-09-12T11:06:26,081 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:26,082 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:26,083 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/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/' 2023-09-12T11:06:26,084 /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/ccfgl0Zv.s 2023-09-12T11:06:26,091 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:26,092 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 2023-09-12T11:06:26,093 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:26,094 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:26,094 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:26,095 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:26,095 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:26,096 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:26,096 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:26,097 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:26,097 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:26,098 #include "..." search starts here: 2023-09-12T11:06:26,098 #include <...> search starts here: 2023-09-12T11:06:26,098 /usr/include/eigen3 2023-09-12T11:06:26,099 include 2023-09-12T11:06:26,099 /usr/include/python3.11 2023-09-12T11:06:26,100 /usr/include/c++/12 2023-09-12T11:06:26,100 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:26,101 /usr/include/c++/12/backward 2023-09-12T11:06:26,101 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:26,102 /usr/local/include 2023-09-12T11:06:26,102 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:26,103 /usr/include 2023-09-12T11:06:26,104 End of search list. 2023-09-12T11:06:26,104 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:26,105 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 2023-09-12T11:06:26,106 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:26,107 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:26,109 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:27,688 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:27,689 from include/openbabel/mol.h:43, 2023-09-12T11:06:27,690 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:27,691 from ./src/formats/nwchemformat.cpp:17: 2023-09-12T11:06:27,691 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:27,692 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:27,693 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:27,693 | ^ 2023-09-12T11:06:27,694 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:27,695 37 | # define UNUSED(x) x 2023-09-12T11:06:27,695 | ^ 2023-09-12T11:06:28,456 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:28,456 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:28,457 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:28,458 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:28,459 | ^ 2023-09-12T11:06:28,459 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:28,460 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:28,461 | ^~~~~~~~ 2023-09-12T11:06:28,463 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:28,463 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:28,464 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:28,464 | ^ 2023-09-12T11:06:28,465 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:28,465 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:28,466 | ^~~~~~~~ 2023-09-12T11:06:28,483 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:28,483 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:28,484 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:28,484 | ^ 2023-09-12T11:06:28,485 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:28,486 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:28,486 | ^~~~~~~~ 2023-09-12T11:06:28,490 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:28,491 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:28,492 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:28,492 | ^ 2023-09-12T11:06:28,493 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:28,494 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:28,495 | ^~~~~~~~ 2023-09-12T11:06:28,664 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:28,665 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:28,666 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:28,667 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:28,667 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:28,668 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:28,669 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:28,670 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:28,671 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:28,672 from include/openbabel/mol.h:35: 2023-09-12T11:06:28,673 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:28,673 131 | struct binary_function 2023-09-12T11:06:28,674 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:28,875 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:28,875 ./src/formats/nwchemformat.cpp:221:72: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:06:28,876 221 | if ((i>=natoms) || (molecule->GetAtom(i+1)->GetAtomicNum() != atoi(vs[2].c_str()))) 2023-09-12T11:06:28,876 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:28,881 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMultipoleMoment(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:28,882 ./src/formats/nwchemformat.cpp:296:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2023-09-12T11:06:28,882 296 | else if (vs[0][0] == '1') 2023-09-12T11:06:28,883 | ^ 2023-09-12T11:06:28,888 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadPartialCharges(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:28,888 ./src/formats/nwchemformat.cpp:413:56: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:06:28,889 413 | if (molecule->GetAtom(i++)->GetAtomicNum() != charge) 2023-09-12T11:06:28,889 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:06:28,899 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMEPCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:28,900 ./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] 2023-09-12T11:06:28,900 561 | if (energies.size() != molecule->NumConformers()) 2023-09-12T11:06:28,901 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:28,942 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadNEBCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:28,943 ./src/formats/nwchemformat.cpp:826:79: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:06:28,944 826 | if (etab.GetAtomicNum(vs[1].substr(0, end_of_symbol).c_str()) != molecule->GetAtom(i+1)->GetAtomicNum()) 2023-09-12T11:06:28,945 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:28,952 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:28,952 ./src/formats/nwchemformat.cpp:914:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T11:06:28,953 914 | if (atoi(buffer) != natoms) 2023-09-12T11:06:28,954 | ~~~~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:06:28,954 ./src/formats/nwchemformat.cpp:924:84: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:06:28,955 924 | if ((vs.size() < 4) || (molecule->GetAtom(i+1)->GetAtomicNum() != etab.GetAtomicNum(vs[0].c_str()))) 2023-09-12T11:06:28,956 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:30,394 ./src/formats/nwchemformat.cpp: At global scope: 2023-09-12T11:06:30,395 ./src/formats/nwchemformat.cpp:104:20: warning: ‘OpenBabel::BETA_ORBITAL_PATTERN’ defined but not used [-Wunused-variable] 2023-09-12T11:06:30,395 104 | static const char* BETA_ORBITAL_PATTERN = "Beta"; 2023-09-12T11:06:30,396 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:33,053 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:33,054 ./src/formats/nwchemformat.cpp:237:18: warning: ‘coordinates’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:33,054 237 | delete[] coordinates; 2023-09-12T11:06:33,055 | ^~~~~~~~~~~ 2023-09-12T11:06:33,056 ./src/formats/nwchemformat.cpp:195:13: note: ‘coordinates’ was declared here 2023-09-12T11:06:33,056 195 | double* coordinates; 2023-09-12T11:06:33,057 | ^~~~~~~~~~~ 2023-09-12T11:06:33,798 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:06:33,799 /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]’: 2023-09-12T11:06:33,799 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:33,800 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:06:33,800 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:34,004 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:34,005 ./src/formats/nwchemformat.cpp:939:21: warning: ‘nbeads’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:34,005 939 | if (bead_number != nbeads) 2023-09-12T11:06:34,006 | ^~ 2023-09-12T11:06:34,007 ./src/formats/nwchemformat.cpp:886:18: note: ‘nbeads’ was declared here 2023-09-12T11:06:34,008 886 | unsigned int nbeads; 2023-09-12T11:06:34,008 | ^~~~~~ 2023-09-12T11:06:34,014 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:06:34,015 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:34,016 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:933:35: 2023-09-12T11:06:34,016 /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 2023-09-12T11:06:34,017 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:06:34,018 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:06:34,288 /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]’: 2023-09-12T11:06:34,288 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:34,289 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:06:34,290 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:34,421 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:34,421 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, 2023-09-12T11:06:34,422 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadPartialCharges(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:418:34: 2023-09-12T11:06:34,423 /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 2023-09-12T11:06:34,424 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:34,425 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:34,676 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:34,677 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, 2023-09-12T11:06:34,678 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadMEPCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:550:43: 2023-09-12T11:06:34,679 /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 2023-09-12T11:06:34,679 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:34,680 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:34,919 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:34,920 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, 2023-09-12T11:06:34,920 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadTDDFTCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:346:34: 2023-09-12T11:06:34,921 /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 2023-09-12T11:06:34,922 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:34,923 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:34,923 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:34,924 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, 2023-09-12T11:06:34,925 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadTDDFTCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:351:46: 2023-09-12T11:06:34,926 /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 2023-09-12T11:06:34,926 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:34,927 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:34,928 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:34,928 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, 2023-09-12T11:06:34,929 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadTDDFTCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:359:46: 2023-09-12T11:06:34,930 /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 2023-09-12T11:06:34,931 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:34,932 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:35,231 /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]’: 2023-09-12T11:06:35,232 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:35,233 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:06:35,233 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:35,471 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:35,472 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, 2023-09-12T11:06:35,473 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadNEBCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:851:35: 2023-09-12T11:06:35,473 /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 2023-09-12T11:06:35,474 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:35,474 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,261 /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]’: 2023-09-12T11:06:36,262 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:36,262 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:06:36,263 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,367 In file included from /usr/include/c++/12/vector:63: 2023-09-12T11:06:36,368 /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*]’: 2023-09-12T11:06:36,369 /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 2023-09-12T11:06:36,369 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2023-09-12T11:06:36,370 | ^~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,371 /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 2023-09-12T11:06:36,458 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]’, 2023-09-12T11:06:36,459 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, 2023-09-12T11:06:36,460 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, 2023-09-12T11:06:36,460 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, 2023-09-12T11:06:36,461 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: 2023-09-12T11:06:36,462 /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 2023-09-12T11:06:36,462 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:36,463 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,572 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]’, 2023-09-12T11:06:36,573 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, 2023-09-12T11:06:36,573 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, 2023-09-12T11:06:36,574 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, 2023-09-12T11:06:36,575 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:06:36,575 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:06:36,576 /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 2023-09-12T11:06:36,577 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:36,577 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,578 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]’, 2023-09-12T11:06:36,579 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, 2023-09-12T11:06:36,580 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, 2023-09-12T11:06:36,581 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, 2023-09-12T11:06:36,581 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:06:36,582 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:06:36,582 /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 2023-09-12T11:06:36,583 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:36,583 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,911 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’, 2023-09-12T11:06:36,912 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:482:31: 2023-09-12T11:06:36,912 /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 2023-09-12T11:06:36,913 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:06:36,914 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:06:36,915 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]’, 2023-09-12T11:06:36,915 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, 2023-09-12T11:06:36,916 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, 2023-09-12T11:06:36,917 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, 2023-09-12T11:06:36,918 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:493:43: 2023-09-12T11:06:36,918 /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 2023-09-12T11:06:36,919 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:36,920 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,920 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]’, 2023-09-12T11:06:36,921 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, 2023-09-12T11:06:36,922 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, 2023-09-12T11:06:36,922 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, 2023-09-12T11:06:36,923 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:502:46: 2023-09-12T11:06:36,924 /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 2023-09-12T11:06:36,925 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:36,926 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:36,926 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]’, 2023-09-12T11:06:36,927 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, 2023-09-12T11:06:36,928 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, 2023-09-12T11:06:36,929 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, 2023-09-12T11:06:36,930 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:504:47: 2023-09-12T11:06:36,930 /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 2023-09-12T11:06:36,931 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:36,932 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:37,502 In member function ‘void OpenBabel::OBMol::SetEnergy(double)’, 2023-09-12T11:06:37,503 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadSinglePointCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:760:24: 2023-09-12T11:06:37,503 include/openbabel/mol.h:418:47: warning: ‘energy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:37,504 418 | void SetEnergy(double energy) { _energy = energy; } 2023-09-12T11:06:37,505 | ~~~~~~~~^~~~~~~~ 2023-09-12T11:06:37,505 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadSinglePointCalculation(std::istream*, OpenBabel::OBMol*)’: 2023-09-12T11:06:37,506 ./src/formats/nwchemformat.cpp:736:12: note: ‘energy’ was declared here 2023-09-12T11:06:37,506 736 | double energy; 2023-09-12T11:06:37,507 | ^~~~~~ 2023-09-12T11:06:37,679 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:37,680 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, 2023-09-12T11:06:37,680 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadGeometryOptimizationCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:606:35: 2023-09-12T11:06:37,681 /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 2023-09-12T11:06:37,682 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:37,683 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,162 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:38,162 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, 2023-09-12T11:06:38,163 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:658:31: 2023-09-12T11:06:38,164 /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 2023-09-12T11:06:38,165 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,165 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,166 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:38,167 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, 2023-09-12T11:06:38,168 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:666:32: 2023-09-12T11:06:38,168 /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 2023-09-12T11:06:38,169 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,170 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,171 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:38,171 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, 2023-09-12T11:06:38,172 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:670:32: 2023-09-12T11:06:38,172 /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 2023-09-12T11:06:38,173 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,173 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,174 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:38,175 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, 2023-09-12T11:06:38,175 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:674:32: 2023-09-12T11:06:38,176 /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 2023-09-12T11:06:38,176 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,177 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,178 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:38,179 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, 2023-09-12T11:06:38,180 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:683:37: 2023-09-12T11:06:38,181 /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 2023-09-12T11:06:38,182 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,182 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:38,183 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:38,184 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:689:36: 2023-09-12T11:06:38,185 /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 2023-09-12T11:06:38,186 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:06:38,186 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:06:38,188 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:38,189 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, 2023-09-12T11:06:38,190 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadFrequencyCalculation(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:702:42: 2023-09-12T11:06:38,191 /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 2023-09-12T11:06:38,191 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:38,192 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:39,346 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/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/' 2023-09-12T11:06:39,347 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/formats/nwchemformat.o /tmp/ccfgl0Zv.s 2023-09-12T11:06:39,351 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:40,192 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/ 2023-09-12T11:06:40,192 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/ 2023-09-12T11:06:40,193 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/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.' 2023-09-12T11:06:40,198 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 2023-09-12T11:06:40,201 Using built-in specs. 2023-09-12T11:06:40,202 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:40,203 Target: arm-linux-gnueabihf 2023-09-12T11:06:40,203 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 2023-09-12T11:06:40,204 Thread model: posix 2023-09-12T11:06:40,205 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:40,205 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:40,206 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:06:40,206 /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/cctqQ5LT.s 2023-09-12T11:06:40,215 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:40,216 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:40,217 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:40,217 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:40,218 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:40,219 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:40,219 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:40,220 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:40,221 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:40,221 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:40,222 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:40,222 #include "..." search starts here: 2023-09-12T11:06:40,223 #include <...> search starts here: 2023-09-12T11:06:40,223 /usr/include/eigen3 2023-09-12T11:06:40,224 include 2023-09-12T11:06:40,224 /usr/include/python3.11 2023-09-12T11:06:40,225 /usr/include/c++/12 2023-09-12T11:06:40,226 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:40,226 /usr/include/c++/12/backward 2023-09-12T11:06:40,227 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:40,227 /usr/local/include 2023-09-12T11:06:40,228 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:40,228 /usr/include 2023-09-12T11:06:40,229 End of search list. 2023-09-12T11:06:40,230 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:40,230 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:40,232 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:40,232 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:40,234 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:41,784 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:41,785 from include/openbabel/mol.h:43, 2023-09-12T11:06:41,786 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:41,786 from ./src/formats/opendxformat.cpp:24: 2023-09-12T11:06:41,787 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:41,787 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:41,788 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:41,789 | ^ 2023-09-12T11:06:41,789 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:41,790 37 | # define UNUSED(x) x 2023-09-12T11:06:41,790 | ^ 2023-09-12T11:06:42,552 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:42,552 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:42,553 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:42,553 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:42,554 | ^ 2023-09-12T11:06:42,555 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:42,555 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:42,556 | ^~~~~~~~ 2023-09-12T11:06:42,557 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:42,558 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:42,558 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:42,559 | ^ 2023-09-12T11:06:42,560 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:42,561 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:42,562 | ^~~~~~~~ 2023-09-12T11:06:42,576 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:42,577 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:42,578 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:42,578 | ^ 2023-09-12T11:06:42,579 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:42,580 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:42,580 | ^~~~~~~~ 2023-09-12T11:06:42,583 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:42,584 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:42,585 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:42,585 | ^ 2023-09-12T11:06:42,586 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:42,586 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:42,587 | ^~~~~~~~ 2023-09-12T11:06:42,756 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:42,757 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:42,757 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:42,758 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:42,758 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:42,759 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:42,760 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:42,760 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:06:42,761 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:06:42,762 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:06:42,762 from /usr/include/c++/12/ios:42, 2023-09-12T11:06:42,763 from /usr/include/c++/12/istream:38, 2023-09-12T11:06:42,764 from /usr/include/c++/12/sstream:38, 2023-09-12T11:06:42,764 from ./src/formats/opendxformat.cpp:21: 2023-09-12T11:06:42,765 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:42,766 131 | struct binary_function 2023-09-12T11:06:42,767 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:42,961 ./src/formats/opendxformat.cpp: In member function ‘virtual int OpenBabel::OBOpenDXCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:06:42,961 ./src/formats/opendxformat.cpp:65:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:06:42,962 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:06:42,963 | ~~~~^ 2023-09-12T11:06:42,964 ./src/formats/opendxformat.cpp:65:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:06:42,964 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:06:42,965 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:06:45,859 In file included from /usr/include/c++/12/vector:70, 2023-09-12T11:06:45,860 from include/openbabel/mol.h:35: 2023-09-12T11:06:45,861 /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]’: 2023-09-12T11:06:45,861 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:45,862 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:06:45,863 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:45,922 /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]’: 2023-09-12T11:06:45,923 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:46,148 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:46,149 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, 2023-09-12T11:06:46,149 inlined from ‘virtual bool OpenBabel::OBOpenDXCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/opendxformat.cpp:149:23: 2023-09-12T11:06:46,150 /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 2023-09-12T11:06:46,151 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:46,151 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:46,152 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:46,153 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, 2023-09-12T11:06:46,153 inlined from ‘virtual bool OpenBabel::OBOpenDXCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/opendxformat.cpp:194:25: 2023-09-12T11:06:46,154 /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 2023-09-12T11:06:46,154 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:46,155 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:46,800 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:06:46,801 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/opendxformat.o /tmp/cctqQ5LT.s 2023-09-12T11:06:46,805 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:06:47,069 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/ 2023-09-12T11:06:47,070 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/ 2023-09-12T11:06:47,070 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/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.' 2023-09-12T11:06:47,072 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/orcaformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/orcaformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:06:47,076 Using built-in specs. 2023-09-12T11:06:47,076 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:06:47,077 Target: arm-linux-gnueabihf 2023-09-12T11:06:47,077 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 2023-09-12T11:06:47,078 Thread model: posix 2023-09-12T11:06:47,079 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:06:47,079 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:06:47,080 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/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/' 2023-09-12T11:06:47,080 /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/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/cctn3C14.s 2023-09-12T11:06:47,090 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:47,091 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:47,092 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:47,093 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:47,093 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:06:47,094 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:06:47,095 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:06:47,095 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:06:47,096 ignoring duplicate directory "/usr/include/" 2023-09-12T11:06:47,096 as it is a non-system directory that duplicates a system directory 2023-09-12T11:06:47,097 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:06:47,097 #include "..." search starts here: 2023-09-12T11:06:47,097 #include <...> search starts here: 2023-09-12T11:06:47,098 /usr/include/eigen3 2023-09-12T11:06:47,098 include 2023-09-12T11:06:47,098 /usr/include/python3.11 2023-09-12T11:06:47,099 /usr/include/c++/12 2023-09-12T11:06:47,099 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:06:47,100 /usr/include/c++/12/backward 2023-09-12T11:06:47,100 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:06:47,100 /usr/local/include 2023-09-12T11:06:47,101 /usr/include/arm-linux-gnueabihf 2023-09-12T11:06:47,101 /usr/include 2023-09-12T11:06:47,102 End of search list. 2023-09-12T11:06:47,102 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:06:47,103 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:06:47,104 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:06:47,104 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:06:47,117 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:06:48,691 In file included from include/openbabel/atom.h:33, 2023-09-12T11:06:48,691 from include/openbabel/mol.h:43, 2023-09-12T11:06:48,692 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:06:48,693 from ./src/formats/orcaformat.cpp:18: 2023-09-12T11:06:48,693 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:06:48,694 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:06:48,695 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:06:48,695 | ^ 2023-09-12T11:06:48,696 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:06:48,697 37 | # define UNUSED(x) x 2023-09-12T11:06:48,698 | ^ 2023-09-12T11:06:49,461 In file included from include/openbabel/mol.h:52: 2023-09-12T11:06:49,462 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:49,462 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:49,463 862 | {return new OBVibrationData(*this);} 2023-09-12T11:06:49,464 | ^ 2023-09-12T11:06:49,464 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:06:49,465 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:06:49,466 | ^~~~~~~~ 2023-09-12T11:06:49,469 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:49,470 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:49,471 907 | {return new OBDOSData(*this);} 2023-09-12T11:06:49,472 | ^ 2023-09-12T11:06:49,472 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:06:49,473 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:06:49,473 | ^~~~~~~~ 2023-09-12T11:06:49,491 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:49,491 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:49,492 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:06:49,492 | ^ 2023-09-12T11:06:49,493 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:06:49,493 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:06:49,494 | ^~~~~~~~ 2023-09-12T11:06:49,499 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:06:49,500 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:06:49,500 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:06:49,501 | ^ 2023-09-12T11:06:49,502 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:06:49,502 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:06:49,503 | ^~~~~~~~ 2023-09-12T11:06:49,673 In file included from include/openbabel/format.h:22, 2023-09-12T11:06:49,674 from include/openbabel/obconversion.h:37, 2023-09-12T11:06:49,675 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:06:49,675 include/openbabel/plugin.h: At global scope: 2023-09-12T11:06:49,676 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:06:49,677 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:06:49,677 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:49,678 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:06:49,678 from /usr/include/c++/12/vector:66, 2023-09-12T11:06:49,679 from include/openbabel/mol.h:35: 2023-09-12T11:06:49,680 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:06:49,680 131 | struct binary_function 2023-09-12T11:06:49,681 | ^~~~~~~~~~~~~~~ 2023-09-12T11:06:50,053 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:50,054 ./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] 2023-09-12T11:06:50,055 338 | while(vs.size() == nColumn+1) { 2023-09-12T11:06:50,056 | ~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:06:50,058 ./src/formats/orcaformat.cpp:353:48: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:06:50,058 353 | for (unsigned int i = 0; i < nColumn; i++) { 2023-09-12T11:06:50,059 | ~~^~~~~~~~~ 2023-09-12T11:06:50,060 ./src/formats/orcaformat.cpp:365:44: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:06:50,061 365 | for (unsigned int i = 0; i < nColumn; i++) { 2023-09-12T11:06:50,061 | ~~^~~~~~~~~ 2023-09-12T11:06:50,077 ./src/formats/orcaformat.cpp:121:12: warning: unused variable ‘energy’ [-Wunused-variable] 2023-09-12T11:06:50,078 121 | double energy=0; 2023-09-12T11:06:50,078 | ^~~~~~ 2023-09-12T11:06:50,079 ./src/formats/orcaformat.cpp:128:9: warning: variable ‘nModeAll’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:06:50,079 128 | int nModeAll = 0; 2023-09-12T11:06:50,080 | ^~~~~~~~ 2023-09-12T11:06:50,098 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:50,098 ./src/formats/orcaformat.cpp:646:10: warning: unused variable ‘buffer’ [-Wunused-variable] 2023-09-12T11:06:50,099 646 | char buffer[BUFF_SIZE]; 2023-09-12T11:06:50,099 | ^~~~~~ 2023-09-12T11:06:54,294 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:06:54,295 /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]’: 2023-09-12T11:06:54,295 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:54,296 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:06:54,297 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:54,356 /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]’: 2023-09-12T11:06:54,357 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:54,866 /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]’: 2023-09-12T11:06:54,867 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:06:54,974 In file included from /usr/include/c++/12/vector:63: 2023-09-12T11:06:54,975 /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*]’: 2023-09-12T11:06:54,975 /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 2023-09-12T11:06:54,976 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2023-09-12T11:06:54,977 | ^~~~~~~~~~~~~~~~ 2023-09-12T11:06:54,978 /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 2023-09-12T11:06:55,014 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]’, 2023-09-12T11:06:55,015 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, 2023-09-12T11:06:55,015 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, 2023-09-12T11:06:55,016 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: 2023-09-12T11:06:55,016 /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 2023-09-12T11:06:55,017 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:55,017 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:55,097 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]’, 2023-09-12T11:06:55,098 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, 2023-09-12T11:06:55,099 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, 2023-09-12T11:06:55,100 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, 2023-09-12T11:06:55,100 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: 2023-09-12T11:06:55,101 /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 2023-09-12T11:06:55,102 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:55,103 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:55,214 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]’, 2023-09-12T11:06:55,215 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, 2023-09-12T11:06:55,215 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, 2023-09-12T11:06:55,216 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, 2023-09-12T11:06:55,216 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:06:55,217 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:06:55,217 /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 2023-09-12T11:06:55,218 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:55,219 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:55,219 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]’, 2023-09-12T11:06:55,220 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, 2023-09-12T11:06:55,221 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, 2023-09-12T11:06:55,222 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, 2023-09-12T11:06:55,222 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2023-09-12T11:06:55,223 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2023-09-12T11:06:55,224 /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 2023-09-12T11:06:55,225 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:55,225 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,760 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:06:58,761 ./src/formats/orcaformat.cpp:210:36: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:58,761 210 | atom->SetVector(x,y,z); //set atom coordinates 2023-09-12T11:06:58,762 | ~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:06:58,762 ./src/formats/orcaformat.cpp:152:13: note: ‘atom’ was declared here 2023-09-12T11:06:58,763 152 | OBAtom *atom; 2023-09-12T11:06:58,764 | ^~~~ 2023-09-12T11:06:58,764 ./src/formats/orcaformat.cpp:207:37: warning: ‘confCoords’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:06:58,765 207 | confCoords[i*3+2] = z; 2023-09-12T11:06:58,765 | ^ 2023-09-12T11:06:58,766 ./src/formats/orcaformat.cpp:139:13: note: ‘confCoords’ was declared here 2023-09-12T11:06:58,766 139 | double* confCoords; 2023-09-12T11:06:58,767 | ^~~~~~~~~~ 2023-09-12T11:06:58,840 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,840 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, 2023-09-12T11:06:58,841 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:242:30: 2023-09-12T11:06:58,842 /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 2023-09-12T11:06:58,842 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,843 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,844 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,845 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, 2023-09-12T11:06:58,845 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:243:35: 2023-09-12T11:06:58,846 /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 2023-09-12T11:06:58,847 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,847 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,848 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,849 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, 2023-09-12T11:06:58,849 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:244:35: 2023-09-12T11:06:58,850 /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 2023-09-12T11:06:58,851 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,851 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,852 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,852 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, 2023-09-12T11:06:58,853 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:259:35: 2023-09-12T11:06:58,853 /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 2023-09-12T11:06:58,854 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,854 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,855 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,855 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, 2023-09-12T11:06:58,856 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:260:40: 2023-09-12T11:06:58,857 /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 2023-09-12T11:06:58,857 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,858 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,859 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,860 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, 2023-09-12T11:06:58,860 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:261:40: 2023-09-12T11:06:58,861 /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 2023-09-12T11:06:58,862 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,862 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,863 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,863 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, 2023-09-12T11:06:58,864 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:314:41: 2023-09-12T11:06:58,865 /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 2023-09-12T11:06:58,866 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,866 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,868 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,869 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, 2023-09-12T11:06:58,869 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:341:36: 2023-09-12T11:06:58,870 /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 2023-09-12T11:06:58,870 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,871 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,873 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,874 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, 2023-09-12T11:06:58,874 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:346:36: 2023-09-12T11:06:58,875 /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 2023-09-12T11:06:58,876 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,876 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,878 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,879 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, 2023-09-12T11:06:58,880 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:351:36: 2023-09-12T11:06:58,881 /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 2023-09-12T11:06:58,881 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,882 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,883 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:58,884 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, 2023-09-12T11:06:58,884 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:355:41: 2023-09-12T11:06:58,885 /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 2023-09-12T11:06:58,886 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,887 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,891 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,892 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, 2023-09-12T11:06:58,892 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:392:38: 2023-09-12T11:06:58,893 /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 2023-09-12T11:06:58,893 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,894 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,895 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,895 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, 2023-09-12T11:06:58,896 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:393:38: 2023-09-12T11:06:58,896 /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 2023-09-12T11:06:58,897 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,897 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,899 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,899 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, 2023-09-12T11:06:58,900 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:410:42: 2023-09-12T11:06:58,901 /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 2023-09-12T11:06:58,902 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,902 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,904 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,904 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, 2023-09-12T11:06:58,905 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:430:35: 2023-09-12T11:06:58,906 /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 2023-09-12T11:06:58,906 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,907 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,908 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,909 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, 2023-09-12T11:06:58,909 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:431:39: 2023-09-12T11:06:58,910 /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 2023-09-12T11:06:58,910 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,911 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,911 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,912 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, 2023-09-12T11:06:58,912 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:432:36: 2023-09-12T11:06:58,913 /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 2023-09-12T11:06:58,913 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,914 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,915 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,916 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, 2023-09-12T11:06:58,916 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:451:35: 2023-09-12T11:06:58,917 /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 2023-09-12T11:06:58,918 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,918 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,919 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,920 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, 2023-09-12T11:06:58,920 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:452:39: 2023-09-12T11:06:58,921 /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 2023-09-12T11:06:58,922 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,922 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,923 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,924 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, 2023-09-12T11:06:58,925 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:453:36: 2023-09-12T11:06:58,925 /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 2023-09-12T11:06:58,926 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,926 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,927 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,927 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, 2023-09-12T11:06:58,928 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:473:37: 2023-09-12T11:06:58,928 /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 2023-09-12T11:06:58,929 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,929 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,930 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,931 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, 2023-09-12T11:06:58,931 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:474:39: 2023-09-12T11:06:58,932 /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 2023-09-12T11:06:58,933 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,934 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,934 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:06:58,935 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, 2023-09-12T11:06:58,935 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:475:44: 2023-09-12T11:06:58,936 /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 2023-09-12T11:06:58,937 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,937 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,938 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:06:58,939 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, 2023-09-12T11:06:58,940 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:492:42: 2023-09-12T11:06:58,940 /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 2023-09-12T11:06:58,941 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:06:58,941 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,943 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:06:58,944 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’, 2023-09-12T11:06:58,944 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:559:36: 2023-09-12T11:06:58,945 /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 2023-09-12T11:06:58,945 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:06:58,946 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:06:58,946 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]’, 2023-09-12T11:06:58,947 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, 2023-09-12T11:06:58,948 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, 2023-09-12T11:06:58,949 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, 2023-09-12T11:06:58,949 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:561:30: 2023-09-12T11:06:58,950 /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 2023-09-12T11:06:58,951 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2023-09-12T11:06:58,951 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:06:58,952 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’, 2023-09-12T11:06:58,953 inlined from ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/orcaformat.cpp:570:39: 2023-09-12T11:06:58,954 /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 2023-09-12T11:06:58,954 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:06:58,955 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:03,258 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/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/' 2023-09-12T11:07:03,258 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/cctn3C14.s 2023-09-12T11:07:03,263 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:04,042 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/ 2023-09-12T11:07:04,042 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/ 2023-09-12T11:07:04,043 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/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.' 2023-09-12T11:07:04,046 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 2023-09-12T11:07:04,050 Using built-in specs. 2023-09-12T11:07:04,051 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:04,051 Target: arm-linux-gnueabihf 2023-09-12T11:07:04,052 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 2023-09-12T11:07:04,053 Thread model: posix 2023-09-12T11:07:04,053 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:04,054 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:04,054 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:07:04,054 /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/ccnZqtjW.s 2023-09-12T11:07:04,064 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:04,065 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 2023-09-12T11:07:04,066 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:04,067 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:04,067 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:04,068 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:04,068 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:04,069 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:04,069 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:04,070 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:04,071 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:04,071 #include "..." search starts here: 2023-09-12T11:07:04,072 #include <...> search starts here: 2023-09-12T11:07:04,073 /usr/include/eigen3 2023-09-12T11:07:04,073 include 2023-09-12T11:07:04,074 /usr/include/python3.11 2023-09-12T11:07:04,074 /usr/include/c++/12 2023-09-12T11:07:04,075 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:04,075 /usr/include/c++/12/backward 2023-09-12T11:07:04,076 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:04,077 /usr/local/include 2023-09-12T11:07:04,077 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:04,078 /usr/include 2023-09-12T11:07:04,078 End of search list. 2023-09-12T11:07:04,079 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:04,079 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:04,081 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:04,081 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:04,091 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:05,657 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:05,657 from include/openbabel/mol.h:43, 2023-09-12T11:07:05,658 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:05,659 from ./src/formats/outformat.cpp:16: 2023-09-12T11:07:05,660 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:05,661 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:05,661 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:05,662 | ^ 2023-09-12T11:07:05,662 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:05,663 37 | # define UNUSED(x) x 2023-09-12T11:07:05,663 | ^ 2023-09-12T11:07:06,432 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:06,432 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:06,433 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:06,433 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:06,434 | ^ 2023-09-12T11:07:06,435 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:06,435 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:06,436 | ^~~~~~~~ 2023-09-12T11:07:06,437 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:06,438 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:06,439 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:06,440 | ^ 2023-09-12T11:07:06,441 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:06,441 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:06,442 | ^~~~~~~~ 2023-09-12T11:07:06,457 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:06,457 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:06,458 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:06,459 | ^ 2023-09-12T11:07:06,460 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:06,460 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:06,461 | ^~~~~~~~ 2023-09-12T11:07:06,464 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:06,464 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:06,465 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:06,466 | ^ 2023-09-12T11:07:06,467 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:06,468 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:06,468 | ^~~~~~~~ 2023-09-12T11:07:06,636 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:06,637 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:06,638 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:06,638 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:06,639 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:06,640 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:06,640 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:06,641 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:06,641 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:06,642 from include/openbabel/mol.h:35: 2023-09-12T11:07:06,642 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:06,643 131 | struct binary_function 2023-09-12T11:07:06,643 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:09,381 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:07:09,382 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/formats/outformat.o /tmp/ccnZqtjW.s 2023-09-12T11:07:09,388 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:09,564 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/ 2023-09-12T11:07:09,565 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/ 2023-09-12T11:07:09,566 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/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.' 2023-09-12T11:07:09,566 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 2023-09-12T11:07:09,571 Using built-in specs. 2023-09-12T11:07:09,572 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:09,572 Target: arm-linux-gnueabihf 2023-09-12T11:07:09,573 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 2023-09-12T11:07:09,573 Thread model: posix 2023-09-12T11:07:09,574 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:09,574 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:09,575 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:07:09,575 /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/ccFH57B8.s 2023-09-12T11:07:09,583 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:09,584 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:09,585 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:09,586 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:09,586 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:09,587 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:09,587 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:09,588 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:09,589 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:09,589 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:09,590 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:09,590 #include "..." search starts here: 2023-09-12T11:07:09,591 #include <...> search starts here: 2023-09-12T11:07:09,592 /usr/include/eigen3 2023-09-12T11:07:09,592 include 2023-09-12T11:07:09,593 /usr/include/python3.11 2023-09-12T11:07:09,594 /usr/include/c++/12 2023-09-12T11:07:09,595 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:09,595 /usr/include/c++/12/backward 2023-09-12T11:07:09,596 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:09,596 /usr/local/include 2023-09-12T11:07:09,597 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:09,597 /usr/include 2023-09-12T11:07:09,598 End of search list. 2023-09-12T11:07:09,598 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:09,598 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 2023-09-12T11:07:09,599 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:09,600 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:09,601 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:11,157 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:11,157 from include/openbabel/mol.h:43, 2023-09-12T11:07:11,158 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:11,158 from ./src/formats/painterformat.cpp:19: 2023-09-12T11:07:11,159 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:11,160 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:11,160 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:11,161 | ^ 2023-09-12T11:07:11,161 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:11,162 37 | # define UNUSED(x) x 2023-09-12T11:07:11,163 | ^ 2023-09-12T11:07:11,927 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:11,928 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:11,929 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:11,930 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:11,930 | ^ 2023-09-12T11:07:11,931 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:11,932 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:11,933 | ^~~~~~~~ 2023-09-12T11:07:11,934 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:11,934 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:11,935 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:11,936 | ^ 2023-09-12T11:07:11,936 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:11,937 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:11,938 | ^~~~~~~~ 2023-09-12T11:07:11,952 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:11,952 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:11,953 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:11,954 | ^ 2023-09-12T11:07:11,955 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:11,955 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:11,956 | ^~~~~~~~ 2023-09-12T11:07:11,958 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:11,959 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:11,959 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:11,960 | ^ 2023-09-12T11:07:11,960 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:11,961 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:11,962 | ^~~~~~~~ 2023-09-12T11:07:12,130 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:12,131 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:12,132 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:12,132 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:12,133 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:12,134 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:12,134 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:12,135 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:12,136 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:12,136 from include/openbabel/mol.h:35: 2023-09-12T11:07:12,137 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:12,138 131 | struct binary_function 2023-09-12T11:07:12,139 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:12,354 In file included from ./src/formats/painterformat.cpp:22: 2023-09-12T11:07:12,355 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2023-09-12T11:07:12,355 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2023-09-12T11:07:12,356 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2023-09-12T11:07:12,357 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:07:12,361 ./src/formats/painterformat.cpp: In member function ‘virtual bool OpenBabel::PainterFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:12,362 ./src/formats/painterformat.cpp:113:12: warning: unused variable ‘ofs’ [-Wunused-variable] 2023-09-12T11:07:12,363 113 | ostream& ofs = *pConv->GetOutStream(); 2023-09-12T11:07:12,364 | ^~~ 2023-09-12T11:07:14,737 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/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/' 2023-09-12T11:07:14,738 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/painterformat.o /tmp/ccFH57B8.s 2023-09-12T11:07:14,745 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:14,918 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/ 2023-09-12T11:07:14,918 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/ 2023-09-12T11:07:14,919 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:07:14,920 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 2023-09-12T11:07:14,924 Using built-in specs. 2023-09-12T11:07:14,925 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:14,926 Target: arm-linux-gnueabihf 2023-09-12T11:07:14,926 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 2023-09-12T11:07:14,927 Thread model: posix 2023-09-12T11:07:14,928 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:14,928 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:14,929 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/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/' 2023-09-12T11:07:14,929 /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/cc5etIFJ.s 2023-09-12T11:07:14,938 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:14,939 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:14,940 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:14,940 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:14,941 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:14,941 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:14,941 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:14,942 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:14,942 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:14,943 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:14,943 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:14,944 #include "..." search starts here: 2023-09-12T11:07:14,944 #include <...> search starts here: 2023-09-12T11:07:14,945 /usr/include/eigen3 2023-09-12T11:07:14,946 include 2023-09-12T11:07:14,946 /usr/include/python3.11 2023-09-12T11:07:14,947 /usr/include/c++/12 2023-09-12T11:07:14,947 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:14,948 /usr/include/c++/12/backward 2023-09-12T11:07:14,949 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:14,949 /usr/local/include 2023-09-12T11:07:14,950 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:14,951 /usr/include 2023-09-12T11:07:14,951 End of search list. 2023-09-12T11:07:14,952 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:14,953 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 2023-09-12T11:07:14,954 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:14,954 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:14,956 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:16,517 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:16,517 from include/openbabel/mol.h:43, 2023-09-12T11:07:16,518 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:16,519 from ./src/formats/pcmodelformat.cpp:16: 2023-09-12T11:07:16,519 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:16,520 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:16,521 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:16,522 | ^ 2023-09-12T11:07:16,522 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:16,523 37 | # define UNUSED(x) x 2023-09-12T11:07:16,524 | ^ 2023-09-12T11:07:17,284 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:17,285 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:17,285 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:17,286 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:17,286 | ^ 2023-09-12T11:07:17,287 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:17,288 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:17,288 | ^~~~~~~~ 2023-09-12T11:07:17,289 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:17,290 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:17,290 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:17,291 | ^ 2023-09-12T11:07:17,292 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:17,292 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:17,293 | ^~~~~~~~ 2023-09-12T11:07:17,308 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:17,309 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:17,310 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:17,310 | ^ 2023-09-12T11:07:17,311 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:17,312 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:17,313 | ^~~~~~~~ 2023-09-12T11:07:17,314 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:17,315 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:17,316 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:17,316 | ^ 2023-09-12T11:07:17,317 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:17,318 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:17,319 | ^~~~~~~~ 2023-09-12T11:07:17,487 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:17,488 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:17,489 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:17,489 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:17,490 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:17,490 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:17,491 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:17,491 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:17,492 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:17,492 from include/openbabel/mol.h:35: 2023-09-12T11:07:17,493 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:17,493 131 | struct binary_function 2023-09-12T11:07:17,494 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:20,695 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/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/' 2023-09-12T11:07:20,695 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/pcmodelformat.o /tmp/cc5etIFJ.s 2023-09-12T11:07:20,700 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:20,916 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/ 2023-09-12T11:07:20,918 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/ 2023-09-12T11:07:20,919 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:07:20,920 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 2023-09-12T11:07:20,923 Using built-in specs. 2023-09-12T11:07:20,923 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:20,924 Target: arm-linux-gnueabihf 2023-09-12T11:07:20,925 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 2023-09-12T11:07:20,925 Thread model: posix 2023-09-12T11:07:20,926 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:20,926 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:20,927 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:07:20,927 /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/cci9GoQv.s 2023-09-12T11:07:20,936 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:20,937 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:20,938 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:20,938 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:20,939 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:20,940 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:20,940 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:20,941 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:20,941 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:20,942 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:20,942 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:20,943 #include "..." search starts here: 2023-09-12T11:07:20,943 #include <...> search starts here: 2023-09-12T11:07:20,944 /usr/include/eigen3 2023-09-12T11:07:20,945 include 2023-09-12T11:07:20,945 /usr/include/python3.11 2023-09-12T11:07:20,946 /usr/include/c++/12 2023-09-12T11:07:20,946 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:20,947 /usr/include/c++/12/backward 2023-09-12T11:07:20,948 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:20,948 /usr/local/include 2023-09-12T11:07:20,949 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:20,950 /usr/include 2023-09-12T11:07:20,950 End of search list. 2023-09-12T11:07:20,951 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:20,952 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:20,953 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:20,953 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:20,954 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:22,518 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:22,519 from include/openbabel/mol.h:43, 2023-09-12T11:07:22,519 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:22,520 from ./src/formats/pdbformat.cpp:17: 2023-09-12T11:07:22,520 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:22,521 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:22,521 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:22,522 | ^ 2023-09-12T11:07:22,522 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:22,523 37 | # define UNUSED(x) x 2023-09-12T11:07:22,523 | ^ 2023-09-12T11:07:23,286 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:23,287 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,288 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,288 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:23,289 | ^ 2023-09-12T11:07:23,290 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:23,290 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:23,291 | ^~~~~~~~ 2023-09-12T11:07:23,292 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,292 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,293 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:23,294 | ^ 2023-09-12T11:07:23,294 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:23,295 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:23,296 | ^~~~~~~~ 2023-09-12T11:07:23,311 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,311 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,312 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:23,313 | ^ 2023-09-12T11:07:23,313 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:23,314 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:23,315 | ^~~~~~~~ 2023-09-12T11:07:23,317 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:23,318 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:23,318 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:23,319 | ^ 2023-09-12T11:07:23,319 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:23,320 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:23,320 | ^~~~~~~~ 2023-09-12T11:07:23,489 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:23,490 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:23,491 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:23,491 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:23,492 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:23,492 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:23,493 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:23,494 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:23,494 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:23,495 from include/openbabel/mol.h:35: 2023-09-12T11:07:23,495 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:23,496 131 | struct binary_function 2023-09-12T11:07:23,497 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:27,170 ./src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:27,171 ./src/formats/pdbformat.cpp:623:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:07:27,172 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:07:27,173 | ^ 2023-09-12T11:07:27,173 ./src/formats/pdbformat.cpp:623:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:07:27,174 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:07:27,175 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:27,175 ./src/formats/pdbformat.cpp:641:70: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:07:27,176 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:07:27,176 | ^ 2023-09-12T11:07:27,177 ./src/formats/pdbformat.cpp:641:29: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:07:27,178 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:07:27,179 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:27,179 ./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=] 2023-09-12T11:07:27,180 678 | snprintf(scharge, 3, "%+d", charge); 2023-09-12T11:07:27,181 | ^~~ 2023-09-12T11:07:27,182 ./src/formats/pdbformat.cpp:678:34: note: directive argument in the range [-32768, 32767] 2023-09-12T11:07:27,182 678 | snprintf(scharge, 3, "%+d", charge); 2023-09-12T11:07:27,183 | ^~~~~ 2023-09-12T11:07:27,183 ./src/formats/pdbformat.cpp:678:21: note: ‘snprintf’ output between 3 and 7 bytes into a destination of size 3 2023-09-12T11:07:27,184 678 | snprintf(scharge, 3, "%+d", charge); 2023-09-12T11:07:27,184 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:30,620 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:07:30,621 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:347:34, 2023-09-12T11:07:30,622 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:07:30,622 ./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] 2023-09-12T11:07:30,623 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:07:30,623 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:30,624 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:07:30,625 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:404:66, 2023-09-12T11:07:30,625 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:07:30,626 ./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] 2023-09-12T11:07:30,627 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:07:30,628 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:30,628 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:07:30,629 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:407:66, 2023-09-12T11:07:30,630 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:07:30,630 ./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] 2023-09-12T11:07:30,631 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:07:30,632 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:30,633 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:07:30,633 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:408:66, 2023-09-12T11:07:30,634 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:07:30,635 ./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] 2023-09-12T11:07:30,636 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:07:30,636 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:30,637 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2023-09-12T11:07:30,638 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:409:66, 2023-09-12T11:07:30,638 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2023-09-12T11:07:30,639 ./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] 2023-09-12T11:07:30,639 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2023-09-12T11:07:30,640 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:32,690 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/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/' 2023-09-12T11:07:32,691 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/formats/pdbformat.o /tmp/cci9GoQv.s 2023-09-12T11:07:32,695 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:33,398 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/ 2023-09-12T11:07:33,398 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/ 2023-09-12T11:07:33,399 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:07:33,402 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/pdbqtformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/pdbqtformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:07:33,406 Using built-in specs. 2023-09-12T11:07:33,407 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:33,407 Target: arm-linux-gnueabihf 2023-09-12T11:07:33,408 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 2023-09-12T11:07:33,408 Thread model: posix 2023-09-12T11:07:33,409 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:33,409 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:33,410 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/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/' 2023-09-12T11:07:33,410 /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/cc8CamXE.s 2023-09-12T11:07:33,419 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:33,420 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 2023-09-12T11:07:33,421 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:33,422 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:33,422 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:33,423 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:33,424 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:33,424 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:33,425 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:33,426 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:33,426 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:33,427 #include "..." search starts here: 2023-09-12T11:07:33,427 #include <...> search starts here: 2023-09-12T11:07:33,428 /usr/include/eigen3 2023-09-12T11:07:33,429 include 2023-09-12T11:07:33,430 /usr/include/python3.11 2023-09-12T11:07:33,431 /usr/include/c++/12 2023-09-12T11:07:33,435 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:33,436 /usr/include/c++/12/backward 2023-09-12T11:07:33,437 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:33,438 /usr/local/include 2023-09-12T11:07:33,439 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:33,440 /usr/include 2023-09-12T11:07:33,441 End of search list. 2023-09-12T11:07:33,441 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:33,442 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:33,443 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:33,444 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:33,444 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:35,022 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:35,022 from include/openbabel/mol.h:43, 2023-09-12T11:07:35,023 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:35,024 from ./src/formats/pdbqtformat.cpp:24: 2023-09-12T11:07:35,024 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:35,025 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:35,025 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:35,026 | ^ 2023-09-12T11:07:35,026 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:35,027 37 | # define UNUSED(x) x 2023-09-12T11:07:35,028 | ^ 2023-09-12T11:07:35,791 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:35,792 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:35,793 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:35,793 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:35,794 | ^ 2023-09-12T11:07:35,795 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:35,795 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:35,796 | ^~~~~~~~ 2023-09-12T11:07:35,797 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:35,798 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:35,799 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:35,799 | ^ 2023-09-12T11:07:35,800 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:35,801 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:35,802 | ^~~~~~~~ 2023-09-12T11:07:35,817 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:35,817 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:35,818 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:35,819 | ^ 2023-09-12T11:07:35,820 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:35,820 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:35,821 | ^~~~~~~~ 2023-09-12T11:07:35,825 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:35,826 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:35,826 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:35,827 | ^ 2023-09-12T11:07:35,827 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:35,828 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:35,829 | ^~~~~~~~ 2023-09-12T11:07:36,003 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:36,003 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:36,004 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:36,005 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:36,005 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:36,006 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:36,006 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:36,007 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:36,008 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:36,008 from include/openbabel/mol.h:35: 2023-09-12T11:07:36,009 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:36,010 131 | struct binary_function 2023-09-12T11:07:36,011 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:36,395 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::OutputTree(OBConversion*, OBMol&, std::ostream&, std::map&, unsigned int, bool, bool)’: 2023-09-12T11:07:36,395 ./src/formats/pdbqtformat.cpp:580:20: warning: unused variable ‘child’ [-Wunused-variable] 2023-09-12T11:07:36,396 580 | unsigned int child=i; 2023-09-12T11:07:36,397 | ^~~~~ 2023-09-12T11:07:36,448 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::ConstructTree(std::map&, std::vector >, unsigned int, const OBMol&, bool)’: 2023-09-12T11:07:36,449 ./src/formats/pdbqtformat.cpp:609:145: warning: unused parameter ‘flexible’ [-Wunused-parameter] 2023-09-12T11:07:36,450 609 | void ConstructTree (map & tree, vector > rigid_fragments, unsigned int root_piece, const OBMol& mol, bool flexible) 2023-09-12T11:07:36,451 | ~~~~~^~~~~~~~ 2023-09-12T11:07:36,467 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::Separate_preserve_charges(OBMol&, std::vector&)’: 2023-09-12T11:07:36,468 ./src/formats/pdbqtformat.cpp:794:9: warning: unused variable ‘fragments’ [-Wunused-variable] 2023-09-12T11:07:36,469 794 | int fragments = 0; 2023-09-12T11:07:36,470 | ^~~~~~~~~ 2023-09-12T11:07:36,537 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::parseAtomRecord(char*, OBMol&, int)’: 2023-09-12T11:07:36,538 ./src/formats/pdbqtformat.cpp:1045:60: warning: unused parameter ‘chainNum’ [-Wunused-parameter] 2023-09-12T11:07:36,538 1045 | static bool parseAtomRecord(char *buffer, OBMol &mol,int chainNum) 2023-09-12T11:07:36,539 | ~~~~^~~~~~~~ 2023-09-12T11:07:38,198 ./src/formats/pdbqtformat.cpp: At global scope: 2023-09-12T11:07:38,199 ./src/formats/pdbqtformat.cpp:747:16: warning: ‘unsigned int OpenBabel::AtomsSoFar(const std::map&, unsigned int)’ defined but not used [-Wunused-function] 2023-09-12T11:07:38,202 747 | unsigned int AtomsSoFar(const map & tree, unsigned int depth) 2023-09-12T11:07:38,203 | ^~~~~~~~~~ 2023-09-12T11:07:40,621 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::OutputAtom(OBAtom*, std::ostream&, unsigned int)’: 2023-09-12T11:07:40,622 ./src/formats/pdbqtformat.cpp:334:52: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:07:40,622 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:07:40,623 | ^ 2023-09-12T11:07:40,623 ./src/formats/pdbqtformat.cpp:334:15: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:07:40,624 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:07:40,625 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:40,625 ./src/formats/pdbqtformat.cpp:351:60: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:07:40,626 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:07:40,626 | ^ 2023-09-12T11:07:40,627 ./src/formats/pdbqtformat.cpp:351:19: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:07:40,628 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:07:40,629 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:43,226 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:07:43,226 /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]’: 2023-09-12T11:07:43,227 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:07:43,228 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:07:43,229 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:48,184 ./src/formats/pdbqtformat.cpp: In member function ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:48,185 ./src/formats/pdbqtformat.cpp:915:22: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 10 equals destination size [-Wstringop-truncation] 2023-09-12T11:07:48,185 915 | strncpy(type_name, etab.GetSymbol(rotBondTable[rotBondId][bondAtomNum]->GetAtomicNum()), sizeof(type_name)); 2023-09-12T11:07:48,186 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:48,320 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:07:48,321 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:07:48,321 inlined from ‘bool OpenBabel::Separate_preserve_charges(OBMol&, std::vector&)’ at ./src/formats/pdbqtformat.cpp:797:23, 2023-09-12T11:07:48,322 inlined from ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbqtformat.cpp:849:32: 2023-09-12T11:07:48,323 /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 2023-09-12T11:07:48,324 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:48,324 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:48,325 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBMol; _Alloc = std::allocator]’, 2023-09-12T11:07:48,325 inlined from ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbqtformat.cpp:845:27: 2023-09-12T11:07:48,326 /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 2023-09-12T11:07:48,327 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:48,327 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:50,414 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/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/' 2023-09-12T11:07:50,415 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/pdbqtformat.o /tmp/cc8CamXE.s 2023-09-12T11:07:50,419 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:51,434 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/ 2023-09-12T11:07:51,435 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/ 2023-09-12T11:07:51,436 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:07:51,440 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 2023-09-12T11:07:51,446 Using built-in specs. 2023-09-12T11:07:51,447 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:51,448 Target: arm-linux-gnueabihf 2023-09-12T11:07:51,448 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 2023-09-12T11:07:51,449 Thread model: posix 2023-09-12T11:07:51,450 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:51,450 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:51,451 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:07:51,452 /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/ccimqmOw.s 2023-09-12T11:07:51,461 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:51,462 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 2023-09-12T11:07:51,464 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:51,465 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:51,466 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:51,467 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:51,469 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:51,471 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:51,472 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:51,474 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:51,476 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:51,477 #include "..." search starts here: 2023-09-12T11:07:51,479 #include <...> search starts here: 2023-09-12T11:07:51,481 /usr/include/eigen3 2023-09-12T11:07:51,483 include 2023-09-12T11:07:51,485 /usr/include/python3.11 2023-09-12T11:07:51,487 /usr/include/c++/12 2023-09-12T11:07:51,489 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:51,491 /usr/include/c++/12/backward 2023-09-12T11:07:51,493 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:51,495 /usr/local/include 2023-09-12T11:07:51,497 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:51,500 /usr/include 2023-09-12T11:07:51,502 End of search list. 2023-09-12T11:07:51,504 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:51,507 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 2023-09-12T11:07:51,513 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:51,516 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:51,518 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:53,145 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:53,145 from include/openbabel/mol.h:43, 2023-09-12T11:07:53,146 from ./src/formats/pointcloudformat.cpp:28: 2023-09-12T11:07:53,146 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:53,147 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:53,148 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:53,148 | ^ 2023-09-12T11:07:53,149 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:53,150 37 | # define UNUSED(x) x 2023-09-12T11:07:53,150 | ^ 2023-09-12T11:07:53,912 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:53,912 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:53,913 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:53,913 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:53,914 | ^ 2023-09-12T11:07:53,915 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:53,915 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:53,916 | ^~~~~~~~ 2023-09-12T11:07:53,917 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:53,918 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:53,918 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:53,919 | ^ 2023-09-12T11:07:53,920 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:53,920 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:53,921 | ^~~~~~~~ 2023-09-12T11:07:53,936 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:53,936 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:53,937 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:53,938 | ^ 2023-09-12T11:07:53,938 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:53,939 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:53,940 | ^~~~~~~~ 2023-09-12T11:07:53,942 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:53,943 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:53,943 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:53,944 | ^ 2023-09-12T11:07:53,944 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:53,945 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:53,946 | ^~~~~~~~ 2023-09-12T11:07:54,115 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:54,115 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:54,116 from ./src/formats/pointcloudformat.cpp:29: 2023-09-12T11:07:54,117 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:54,117 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:54,118 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:54,118 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:54,119 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:54,120 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:54,121 from include/openbabel/mol.h:35: 2023-09-12T11:07:54,121 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:54,122 131 | struct binary_function 2023-09-12T11:07:54,123 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:54,314 ./src/formats/pointcloudformat.cpp: In member function ‘virtual int OpenBabel::PointCloudFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:07:54,314 ./src/formats/pointcloudformat.cpp:104:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:07:54,315 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:07:54,316 | ~~~~^ 2023-09-12T11:07:54,317 ./src/formats/pointcloudformat.cpp:104:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:07:54,317 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:07:54,318 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:07:54,336 ./src/formats/pointcloudformat.cpp: In member function ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:07:54,336 ./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] 2023-09-12T11:07:54,337 217 | for( int j = 0; j < radius_mult_list.size(); j++ ) { 2023-09-12T11:07:54,338 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:56,593 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:07:56,594 /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]’: 2023-09-12T11:07:56,594 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:07:56,595 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:07:56,596 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:56,647 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:07:56,648 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:07:56,648 inlined from ‘bool OpenBabel::conditional_add(std::vector&, vector3, double)’ at ./src/formats/pointcloudformat.cpp:150:19: 2023-09-12T11:07:56,649 /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 2023-09-12T11:07:56,650 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:56,650 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:56,682 /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]’: 2023-09-12T11:07:56,683 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:07:56,683 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:07:56,684 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:56,732 /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]’: 2023-09-12T11:07:56,733 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:07:56,876 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:07:56,877 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:196:63: 2023-09-12T11:07:56,878 /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 2023-09-12T11:07:56,879 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:56,879 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:56,880 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:07:56,881 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:206:59: 2023-09-12T11:07:56,882 /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 2023-09-12T11:07:56,882 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:56,883 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:56,884 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:07:56,884 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, 2023-09-12T11:07:56,885 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:211:68: 2023-09-12T11:07:56,886 /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 2023-09-12T11:07:56,887 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:07:56,887 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:56,887 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:07:56,888 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, 2023-09-12T11:07:56,888 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:213:29: 2023-09-12T11:07:56,889 /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 2023-09-12T11:07:56,889 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:07:56,890 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:07:56,890 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:07:56,891 inlined from ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pointcloudformat.cpp:260:38: 2023-09-12T11:07:56,892 /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 2023-09-12T11:07:56,892 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:07:56,893 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:07:57,224 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:07:57,224 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/ccimqmOw.s 2023-09-12T11:07:57,228 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:07:57,417 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/ 2023-09-12T11:07:57,419 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/ 2023-09-12T11:07:57,420 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:07:57,420 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 2023-09-12T11:07:57,423 Using built-in specs. 2023-09-12T11:07:57,424 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:07:57,424 Target: arm-linux-gnueabihf 2023-09-12T11:07:57,425 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 2023-09-12T11:07:57,425 Thread model: posix 2023-09-12T11:07:57,426 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:07:57,426 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:07:57,427 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/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/' 2023-09-12T11:07:57,427 /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/ccSjz44B.s 2023-09-12T11:07:57,436 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:57,437 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:57,438 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:57,438 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:57,439 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:07:57,440 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:07:57,440 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:07:57,441 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:07:57,441 ignoring duplicate directory "/usr/include/" 2023-09-12T11:07:57,442 as it is a non-system directory that duplicates a system directory 2023-09-12T11:07:57,443 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:07:57,443 #include "..." search starts here: 2023-09-12T11:07:57,444 #include <...> search starts here: 2023-09-12T11:07:57,444 /usr/include/eigen3 2023-09-12T11:07:57,445 include 2023-09-12T11:07:57,445 /usr/include/python3.11 2023-09-12T11:07:57,445 /usr/include/c++/12 2023-09-12T11:07:57,446 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:07:57,446 /usr/include/c++/12/backward 2023-09-12T11:07:57,447 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:07:57,447 /usr/local/include 2023-09-12T11:07:57,448 /usr/include/arm-linux-gnueabihf 2023-09-12T11:07:57,448 /usr/include 2023-09-12T11:07:57,448 End of search list. 2023-09-12T11:07:57,449 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:07:57,449 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:07:57,450 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:07:57,451 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:07:57,455 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:07:59,013 In file included from include/openbabel/atom.h:33, 2023-09-12T11:07:59,013 from include/openbabel/mol.h:43, 2023-09-12T11:07:59,014 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:07:59,014 from ./src/formats/posformat.cpp:15: 2023-09-12T11:07:59,015 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:07:59,016 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:07:59,017 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:07:59,018 | ^ 2023-09-12T11:07:59,018 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:07:59,019 37 | # define UNUSED(x) x 2023-09-12T11:07:59,020 | ^ 2023-09-12T11:07:59,781 In file included from include/openbabel/mol.h:52: 2023-09-12T11:07:59,781 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:59,782 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:59,783 862 | {return new OBVibrationData(*this);} 2023-09-12T11:07:59,784 | ^ 2023-09-12T11:07:59,784 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:07:59,785 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:07:59,786 | ^~~~~~~~ 2023-09-12T11:07:59,786 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:59,787 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:59,788 907 | {return new OBDOSData(*this);} 2023-09-12T11:07:59,788 | ^ 2023-09-12T11:07:59,789 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:07:59,790 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:07:59,791 | ^~~~~~~~ 2023-09-12T11:07:59,806 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:59,806 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:59,807 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:07:59,807 | ^ 2023-09-12T11:07:59,808 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:07:59,809 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:07:59,809 | ^~~~~~~~ 2023-09-12T11:07:59,813 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:07:59,814 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:07:59,814 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:07:59,815 | ^ 2023-09-12T11:07:59,815 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:07:59,816 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:07:59,817 | ^~~~~~~~ 2023-09-12T11:07:59,987 In file included from include/openbabel/format.h:22, 2023-09-12T11:07:59,988 from include/openbabel/obconversion.h:37, 2023-09-12T11:07:59,989 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:07:59,990 include/openbabel/plugin.h: At global scope: 2023-09-12T11:07:59,990 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:07:59,991 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:07:59,992 | ^~~~~~~~~~~~~~~ 2023-09-12T11:07:59,992 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:07:59,993 from /usr/include/c++/12/vector:66, 2023-09-12T11:07:59,994 from include/openbabel/mol.h:35: 2023-09-12T11:07:59,994 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:07:59,995 131 | struct binary_function 2023-09-12T11:07:59,995 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:00,190 ./src/formats/posformat.cpp: In member function ‘virtual bool OpenBabel::POSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:00,191 ./src/formats/posformat.cpp:101:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2023-09-12T11:08:00,191 101 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2023-09-12T11:08:00,192 | ~^ ~~~~~~~ 2023-09-12T11:08:00,193 | | | 2023-09-12T11:08:00,194 | | unsigned int* 2023-09-12T11:08:00,194 | int* 2023-09-12T11:08:00,195 | %d 2023-09-12T11:08:03,383 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:03,383 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/ccSjz44B.s 2023-09-12T11:08:03,388 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:03,619 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/ 2023-09-12T11:08:03,619 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/ 2023-09-12T11:08:03,620 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/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.' 2023-09-12T11:08:03,621 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 2023-09-12T11:08:03,625 Using built-in specs. 2023-09-12T11:08:03,626 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:03,626 Target: arm-linux-gnueabihf 2023-09-12T11:08:03,627 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 2023-09-12T11:08:03,628 Thread model: posix 2023-09-12T11:08:03,628 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:03,629 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:03,629 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:03,630 /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/ccqy7EZX.s 2023-09-12T11:08:03,639 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:03,640 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:03,641 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:03,641 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:03,642 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:03,642 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:03,642 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:03,643 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:03,644 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:03,644 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:03,645 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:03,646 #include "..." search starts here: 2023-09-12T11:08:03,646 #include <...> search starts here: 2023-09-12T11:08:03,647 /usr/include/eigen3 2023-09-12T11:08:03,648 include 2023-09-12T11:08:03,648 /usr/include/python3.11 2023-09-12T11:08:03,649 /usr/include/c++/12 2023-09-12T11:08:03,650 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:03,650 /usr/include/c++/12/backward 2023-09-12T11:08:03,651 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:03,652 /usr/local/include 2023-09-12T11:08:03,652 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:03,653 /usr/include 2023-09-12T11:08:03,653 End of search list. 2023-09-12T11:08:03,654 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:03,655 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:03,656 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:03,656 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:03,657 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:05,226 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:05,226 from include/openbabel/mol.h:43, 2023-09-12T11:08:05,227 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:05,227 from ./src/formats/povrayformat.cpp:23: 2023-09-12T11:08:05,228 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:05,229 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:05,230 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:05,231 | ^ 2023-09-12T11:08:05,231 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:05,232 37 | # define UNUSED(x) x 2023-09-12T11:08:05,232 | ^ 2023-09-12T11:08:05,991 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:05,992 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:05,992 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:05,993 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:05,993 | ^ 2023-09-12T11:08:05,994 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:05,995 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:05,995 | ^~~~~~~~ 2023-09-12T11:08:05,996 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:05,997 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:05,998 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:05,998 | ^ 2023-09-12T11:08:05,999 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:05,999 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:06,000 | ^~~~~~~~ 2023-09-12T11:08:06,015 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:06,016 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:06,017 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:06,017 | ^ 2023-09-12T11:08:06,018 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:06,019 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:06,019 | ^~~~~~~~ 2023-09-12T11:08:06,022 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:06,022 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:06,023 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:06,024 | ^ 2023-09-12T11:08:06,024 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:06,025 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:06,026 | ^~~~~~~~ 2023-09-12T11:08:06,194 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:06,195 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:06,195 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:06,196 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:06,196 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:06,197 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:06,197 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:06,198 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:06,199 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:06,199 from include/openbabel/mol.h:35: 2023-09-12T11:08:06,200 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:06,200 131 | struct binary_function 2023-09-12T11:08:06,201 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:06,470 ./src/formats/povrayformat.cpp: In member function ‘void OpenBabel::PovrayFormat::OutputHeader(std::ostream&, OpenBabel::OBMol&, std::string)’: 2023-09-12T11:08:06,470 ./src/formats/povrayformat.cpp:168:12: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:08:06,471 168 | size_t time_res; /* Result of strftime */ 2023-09-12T11:08:06,471 | ^~~~~~~~ 2023-09-12T11:08:06,472 ./src/formats/povrayformat.cpp:164:68: warning: unused parameter ‘prefix’ [-Wunused-parameter] 2023-09-12T11:08:06,473 164 | void PovrayFormat::OutputHeader(ostream &ofs, OBMol &mol, string prefix) 2023-09-12T11:08:06,474 | ~~~~~~~^~~~~~ 2023-09-12T11:08:06,503 ./src/formats/povrayformat.cpp: In function ‘void OpenBabel::OutputCSTBonds(std::ostream&, OBMol&, std::string)’: 2023-09-12T11:08:06,504 ./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] 2023-09-12T11:08:06,505 521 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2023-09-12T11:08:06,505 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:06,506 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T11:08:06,507 /usr/include/c++/12/backward/binders.h:136:5: note: declared here 2023-09-12T11:08:06,508 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:08:06,508 | ^~~~~~~ 2023-09-12T11:08:06,518 ./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] 2023-09-12T11:08:06,519 582 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2023-09-12T11:08:06,519 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:06,520 /usr/include/c++/12/backward/binders.h:136:5: note: declared here 2023-09-12T11:08:06,521 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:08:06,522 | ^~~~~~~ 2023-09-12T11:08:06,584 ./src/formats/povrayformat.cpp: In member function ‘virtual bool OpenBabel::PovrayFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:06,585 ./src/formats/povrayformat.cpp:802:17: warning: unused variable ‘title’ [-Wunused-variable] 2023-09-12T11:08:06,586 802 | const char* title = pmol->GetTitle(); 2023-09-12T11:08:06,586 | ^~~~~ 2023-09-12T11:08:12,543 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:12,543 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/ccqy7EZX.s 2023-09-12T11:08:12,548 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:12,995 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/ 2023-09-12T11:08:12,996 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/ 2023-09-12T11:08:12,996 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:08:12,998 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 2023-09-12T11:08:13,002 Using built-in specs. 2023-09-12T11:08:13,004 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:13,004 Target: arm-linux-gnueabihf 2023-09-12T11:08:13,005 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 2023-09-12T11:08:13,006 Thread model: posix 2023-09-12T11:08:13,006 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:13,007 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:13,007 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:13,008 /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/ccw3DtBK.s 2023-09-12T11:08:13,015 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:13,016 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:13,017 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:13,018 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:13,018 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:13,019 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:13,019 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:13,020 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:13,021 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:13,021 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:13,022 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:13,023 #include "..." search starts here: 2023-09-12T11:08:13,023 #include <...> search starts here: 2023-09-12T11:08:13,024 /usr/include/eigen3 2023-09-12T11:08:13,025 include 2023-09-12T11:08:13,025 /usr/include/python3.11 2023-09-12T11:08:13,026 /usr/include/c++/12 2023-09-12T11:08:13,027 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:13,027 /usr/include/c++/12/backward 2023-09-12T11:08:13,028 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:13,028 /usr/local/include 2023-09-12T11:08:13,029 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:13,030 /usr/include 2023-09-12T11:08:13,030 End of search list. 2023-09-12T11:08:13,031 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:13,032 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 2023-09-12T11:08:13,033 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:13,034 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:13,036 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:14,598 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:14,598 from include/openbabel/mol.h:43, 2023-09-12T11:08:14,599 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:14,600 from ./src/formats/pqrformat.cpp:16: 2023-09-12T11:08:14,601 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:14,602 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:14,602 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:14,603 | ^ 2023-09-12T11:08:14,603 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:14,604 37 | # define UNUSED(x) x 2023-09-12T11:08:14,604 | ^ 2023-09-12T11:08:15,364 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:15,365 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:15,365 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:15,366 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:15,367 | ^ 2023-09-12T11:08:15,367 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:15,368 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:15,368 | ^~~~~~~~ 2023-09-12T11:08:15,370 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:15,370 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:15,371 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:15,371 | ^ 2023-09-12T11:08:15,372 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:15,373 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:15,374 | ^~~~~~~~ 2023-09-12T11:08:15,389 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:15,390 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:15,391 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:15,392 | ^ 2023-09-12T11:08:15,392 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:15,393 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:15,394 | ^~~~~~~~ 2023-09-12T11:08:15,395 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:15,396 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:15,397 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:15,398 | ^ 2023-09-12T11:08:15,398 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:15,399 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:15,400 | ^~~~~~~~ 2023-09-12T11:08:15,568 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:15,569 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:15,569 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:15,570 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:15,571 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:15,571 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:15,572 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:15,572 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:15,573 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:15,573 from include/openbabel/mol.h:35: 2023-09-12T11:08:15,574 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:15,574 131 | struct binary_function 2023-09-12T11:08:15,575 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:15,785 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomCharge(char*, OBMol&)’: 2023-09-12T11:08:15,786 ./src/formats/pqrformat.cpp:196:13: warning: unused variable ‘atom’ [-Wunused-variable] 2023-09-12T11:08:15,786 196 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2023-09-12T11:08:15,787 | ^~~~ 2023-09-12T11:08:15,788 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomRadius(char*, OBMol&)’: 2023-09-12T11:08:15,788 ./src/formats/pqrformat.cpp:211:13: warning: unused variable ‘atom’ [-Wunused-variable] 2023-09-12T11:08:15,789 211 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2023-09-12T11:08:15,790 | ^~~~ 2023-09-12T11:08:18,167 ./src/formats/pqrformat.cpp: In member function ‘virtual bool OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:18,168 ./src/formats/pqrformat.cpp:501:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2023-09-12T11:08:18,168 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:08:18,169 | ^ 2023-09-12T11:08:18,170 ./src/formats/pqrformat.cpp:501:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2023-09-12T11:08:18,171 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2023-09-12T11:08:18,171 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:18,172 ./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=] 2023-09-12T11:08:18,173 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:08:18,173 | ^~~~ ~~~ 2023-09-12T11:08:18,174 ./src/formats/pqrformat.cpp:518:29: note: ‘snprintf’ output between 5 and 17 bytes into a destination of size 10 2023-09-12T11:08:18,175 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2023-09-12T11:08:18,176 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:18,915 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:08:18,915 /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]’: 2023-09-12T11:08:18,916 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:18,917 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:08:18,917 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:20,805 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:20,805 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, 2023-09-12T11:08:20,806 inlined from ‘virtual bool OpenBabel::PQRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pqrformat.cpp:135:30: 2023-09-12T11:08:20,806 /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 2023-09-12T11:08:20,807 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:20,807 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:20,808 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:20,809 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, 2023-09-12T11:08:20,809 inlined from ‘virtual bool OpenBabel::PQRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pqrformat.cpp:136:28: 2023-09-12T11:08:20,810 /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 2023-09-12T11:08:20,811 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:20,811 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:21,614 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/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/' 2023-09-12T11:08:21,615 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/ccw3DtBK.s 2023-09-12T11:08:21,623 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:22,091 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/ 2023-09-12T11:08:22,091 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/ 2023-09-12T11:08:22,092 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:08:22,094 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 2023-09-12T11:08:22,099 Using built-in specs. 2023-09-12T11:08:22,099 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:22,100 Target: arm-linux-gnueabihf 2023-09-12T11:08:22,101 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 2023-09-12T11:08:22,101 Thread model: posix 2023-09-12T11:08:22,102 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:22,102 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:22,103 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:22,103 /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/ccyxYk17.s 2023-09-12T11:08:22,112 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:22,113 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:22,114 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:22,115 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:22,115 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:22,116 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:22,117 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:22,117 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:22,118 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:22,118 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:22,119 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:22,119 #include "..." search starts here: 2023-09-12T11:08:22,120 #include <...> search starts here: 2023-09-12T11:08:22,120 /usr/include/eigen3 2023-09-12T11:08:22,120 include 2023-09-12T11:08:22,121 /usr/include/python3.11 2023-09-12T11:08:22,121 /usr/include/c++/12 2023-09-12T11:08:22,122 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:22,122 /usr/include/c++/12/backward 2023-09-12T11:08:22,122 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:22,123 /usr/local/include 2023-09-12T11:08:22,123 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:22,124 /usr/include 2023-09-12T11:08:22,124 End of search list. 2023-09-12T11:08:22,125 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:22,125 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:22,126 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:22,126 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:22,131 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:23,692 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:23,692 from include/openbabel/mol.h:43, 2023-09-12T11:08:23,693 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:23,694 from ./src/formats/pwscfformat.cpp:16: 2023-09-12T11:08:23,695 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:23,695 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:23,696 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:23,697 | ^ 2023-09-12T11:08:23,698 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:23,699 37 | # define UNUSED(x) x 2023-09-12T11:08:23,699 | ^ 2023-09-12T11:08:24,458 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:24,459 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:24,459 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:24,460 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:24,461 | ^ 2023-09-12T11:08:24,462 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:24,462 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:24,463 | ^~~~~~~~ 2023-09-12T11:08:24,464 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:24,464 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:24,465 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:24,466 | ^ 2023-09-12T11:08:24,467 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:24,467 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:24,468 | ^~~~~~~~ 2023-09-12T11:08:24,482 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:24,483 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:24,484 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:24,484 | ^ 2023-09-12T11:08:24,485 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:24,485 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:24,486 | ^~~~~~~~ 2023-09-12T11:08:24,489 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:24,489 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:24,490 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:24,490 | ^ 2023-09-12T11:08:24,491 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:24,492 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:24,493 | ^~~~~~~~ 2023-09-12T11:08:24,661 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:24,661 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:24,662 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:24,663 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:24,664 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:24,664 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:24,665 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:24,666 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:24,666 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:24,667 from include/openbabel/mol.h:35: 2023-09-12T11:08:24,668 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:24,668 131 | struct binary_function 2023-09-12T11:08:24,669 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:24,859 ./src/formats/pwscfformat.cpp: In member function ‘virtual int OpenBabel::PWscfFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:08:24,860 ./src/formats/pwscfformat.cpp:51:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:08:24,861 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:08:24,861 | ~~~~^ 2023-09-12T11:08:24,862 ./src/formats/pwscfformat.cpp:51:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:08:24,863 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:08:24,863 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:08:27,453 ./src/formats/pwscfformat.cpp: In member function ‘virtual bool OpenBabel::PWscfFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:27,454 ./src/formats/pwscfformat.cpp:276:15: warning: ‘pv’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:27,455 276 | snprintf(tag, BUFF_SIZE, "%f", pv_kcal_per_mole); 2023-09-12T11:08:27,455 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:27,456 ./src/formats/pwscfformat.cpp:90:22: note: ‘pv’ was declared here 2023-09-12T11:08:27,456 90 | double enthalpy, pv; 2023-09-12T11:08:27,457 | ^~ 2023-09-12T11:08:27,457 ./src/formats/pwscfformat.cpp:274:15: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:08:27,458 274 | snprintf(tag, BUFF_SIZE, "%f", en_kcal_per_mole); 2023-09-12T11:08:27,459 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:27,459 ./src/formats/pwscfformat.cpp:90:12: note: ‘enthalpy’ was declared here 2023-09-12T11:08:27,460 90 | double enthalpy, pv; 2023-09-12T11:08:27,460 | ^~~~~~~~ 2023-09-12T11:08:28,307 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:28,308 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/ccyxYk17.s 2023-09-12T11:08:28,312 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:28,544 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/ 2023-09-12T11:08:28,545 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/ 2023-09-12T11:08:28,546 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/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.' 2023-09-12T11:08:28,547 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 2023-09-12T11:08:28,551 Using built-in specs. 2023-09-12T11:08:28,552 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:28,552 Target: arm-linux-gnueabihf 2023-09-12T11:08:28,553 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 2023-09-12T11:08:28,553 Thread model: posix 2023-09-12T11:08:28,554 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:28,554 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:28,555 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/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/' 2023-09-12T11:08:28,555 /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/cc0uatN9.s 2023-09-12T11:08:28,564 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:28,564 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:28,565 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:28,566 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:28,566 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:28,567 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:28,567 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:28,568 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:28,569 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:28,569 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:28,570 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:28,570 #include "..." search starts here: 2023-09-12T11:08:28,571 #include <...> search starts here: 2023-09-12T11:08:28,571 /usr/include/eigen3 2023-09-12T11:08:28,572 include 2023-09-12T11:08:28,573 /usr/include/python3.11 2023-09-12T11:08:28,573 /usr/include/c++/12 2023-09-12T11:08:28,574 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:28,575 /usr/include/c++/12/backward 2023-09-12T11:08:28,575 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:28,576 /usr/local/include 2023-09-12T11:08:28,576 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:28,577 /usr/include 2023-09-12T11:08:28,577 End of search list. 2023-09-12T11:08:28,577 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:28,578 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:28,578 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:28,579 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:28,582 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:30,144 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:30,145 from include/openbabel/mol.h:43, 2023-09-12T11:08:30,145 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:30,146 from ./src/formats/qchemformat.cpp:17: 2023-09-12T11:08:30,146 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:30,147 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:30,147 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:30,148 | ^ 2023-09-12T11:08:30,149 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:30,149 37 | # define UNUSED(x) x 2023-09-12T11:08:30,150 | ^ 2023-09-12T11:08:30,913 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:30,913 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,914 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,915 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:30,916 | ^ 2023-09-12T11:08:30,916 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:30,917 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:30,918 | ^~~~~~~~ 2023-09-12T11:08:30,918 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,919 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,920 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:30,920 | ^ 2023-09-12T11:08:30,921 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:30,922 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:30,922 | ^~~~~~~~ 2023-09-12T11:08:30,937 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,938 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,939 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:30,940 | ^ 2023-09-12T11:08:30,941 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:30,941 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:30,942 | ^~~~~~~~ 2023-09-12T11:08:30,944 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:30,945 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:30,946 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:30,946 | ^ 2023-09-12T11:08:30,947 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:30,947 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:30,948 | ^~~~~~~~ 2023-09-12T11:08:31,118 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:31,119 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:31,120 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:31,120 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:31,121 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:31,122 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:31,123 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:31,123 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:31,124 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:31,125 from include/openbabel/mol.h:35: 2023-09-12T11:08:31,125 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:31,126 131 | struct binary_function 2023-09-12T11:08:31,127 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:34,579 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:08:34,580 /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]’: 2023-09-12T11:08:34,580 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:34,581 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:08:34,582 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:34,641 /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]’: 2023-09-12T11:08:34,641 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:08:35,512 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:35,513 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, 2023-09-12T11:08:35,514 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:217:36: 2023-09-12T11:08:35,515 /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 2023-09-12T11:08:35,515 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:35,516 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:35,516 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:08:35,517 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, 2023-09-12T11:08:35,517 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:227:36: 2023-09-12T11:08:35,518 /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 2023-09-12T11:08:35,518 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:35,519 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:35,520 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:08:35,520 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, 2023-09-12T11:08:35,521 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:245:33: 2023-09-12T11:08:35,522 /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 2023-09-12T11:08:35,523 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:35,523 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:35,524 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:08:35,525 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, 2023-09-12T11:08:35,525 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:247:33: 2023-09-12T11:08:35,526 /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 2023-09-12T11:08:35,527 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:35,527 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:35,528 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:08:35,529 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, 2023-09-12T11:08:35,530 inlined from ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/qchemformat.cpp:249:33: 2023-09-12T11:08:35,531 /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 2023-09-12T11:08:35,531 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:08:35,532 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:36,807 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/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/' 2023-09-12T11:08:36,808 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/cc0uatN9.s 2023-09-12T11:08:36,812 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:37,213 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/ 2023-09-12T11:08:37,214 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/ 2023-09-12T11:08:37,214 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/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.' 2023-09-12T11:08:37,216 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 2023-09-12T11:08:37,220 Using built-in specs. 2023-09-12T11:08:37,221 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:37,221 Target: arm-linux-gnueabihf 2023-09-12T11:08:37,222 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 2023-09-12T11:08:37,222 Thread model: posix 2023-09-12T11:08:37,223 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:37,224 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:37,224 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:37,225 /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/cc8RDhe9.s 2023-09-12T11:08:37,233 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:37,233 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:37,234 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:37,235 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:37,236 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:37,236 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:37,237 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:37,238 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:37,238 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:37,239 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:37,239 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:37,240 #include "..." search starts here: 2023-09-12T11:08:37,240 #include <...> search starts here: 2023-09-12T11:08:37,241 /usr/include/eigen3 2023-09-12T11:08:37,242 include 2023-09-12T11:08:37,242 /usr/include/python3.11 2023-09-12T11:08:37,243 /usr/include/c++/12 2023-09-12T11:08:37,243 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:37,244 /usr/include/c++/12/backward 2023-09-12T11:08:37,244 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:37,245 /usr/local/include 2023-09-12T11:08:37,245 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:37,246 /usr/include 2023-09-12T11:08:37,247 End of search list. 2023-09-12T11:08:37,247 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:37,248 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:37,249 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:37,250 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:37,253 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:38,828 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:38,829 from include/openbabel/mol.h:43, 2023-09-12T11:08:38,829 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:08:38,830 from ./src/formats/reportformat.cpp:23: 2023-09-12T11:08:38,830 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:38,831 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:38,831 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:38,832 | ^ 2023-09-12T11:08:38,832 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:38,833 37 | # define UNUSED(x) x 2023-09-12T11:08:38,833 | ^ 2023-09-12T11:08:39,599 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:39,600 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:39,600 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:39,601 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:39,601 | ^ 2023-09-12T11:08:39,602 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:39,603 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:39,604 | ^~~~~~~~ 2023-09-12T11:08:39,604 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:39,605 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:39,606 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:39,607 | ^ 2023-09-12T11:08:39,608 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:39,608 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:39,609 | ^~~~~~~~ 2023-09-12T11:08:39,624 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:39,624 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:39,625 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:39,626 | ^ 2023-09-12T11:08:39,626 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:39,627 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:39,628 | ^~~~~~~~ 2023-09-12T11:08:39,630 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:39,631 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:39,632 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:39,633 | ^ 2023-09-12T11:08:39,633 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:39,634 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:39,634 | ^~~~~~~~ 2023-09-12T11:08:39,803 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:39,804 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:39,804 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:08:39,805 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:39,805 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:39,806 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:39,806 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:39,807 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:08:39,807 from /usr/include/c++/12/vector:66, 2023-09-12T11:08:39,808 from include/openbabel/mol.h:35: 2023-09-12T11:08:39,809 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:39,809 131 | struct binary_function 2023-09-12T11:08:39,810 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:42,806 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:42,807 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/cc8RDhe9.s 2023-09-12T11:08:42,811 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:43,005 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/ 2023-09-12T11:08:43,005 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/ 2023-09-12T11:08:43,006 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/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.' 2023-09-12T11:08:43,007 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/rsmiformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/rsmiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:43,011 Using built-in specs. 2023-09-12T11:08:43,012 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:43,013 Target: arm-linux-gnueabihf 2023-09-12T11:08:43,013 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 2023-09-12T11:08:43,014 Thread model: posix 2023-09-12T11:08:43,014 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:43,015 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:43,015 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:43,016 /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/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/ccCulpd9.s 2023-09-12T11:08:43,025 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:43,025 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 2023-09-12T11:08:43,026 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:43,027 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:43,027 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:43,028 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:43,029 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:43,029 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:43,030 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:43,031 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:43,032 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:43,032 #include "..." search starts here: 2023-09-12T11:08:43,032 #include <...> search starts here: 2023-09-12T11:08:43,033 /usr/include/eigen3 2023-09-12T11:08:43,033 include 2023-09-12T11:08:43,034 /usr/include/python3.11 2023-09-12T11:08:43,034 /usr/include/c++/12 2023-09-12T11:08:43,035 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:43,035 /usr/include/c++/12/backward 2023-09-12T11:08:43,036 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:43,036 /usr/local/include 2023-09-12T11:08:43,037 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:43,037 /usr/include 2023-09-12T11:08:43,037 End of search list. 2023-09-12T11:08:43,038 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:43,038 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:43,039 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:43,040 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:43,044 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:45,186 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:45,203 from include/openbabel/mol.h:43, 2023-09-12T11:08:45,228 from ./src/formats/rsmiformat.cpp:19: 2023-09-12T11:08:45,280 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:45,296 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:45,297 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:45,298 | ^ 2023-09-12T11:08:45,298 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:45,299 37 | # define UNUSED(x) x 2023-09-12T11:08:45,300 | ^ 2023-09-12T11:08:45,953 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:45,954 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:45,955 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:45,956 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:45,956 | ^ 2023-09-12T11:08:45,957 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:45,958 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:45,959 | ^~~~~~~~ 2023-09-12T11:08:45,959 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:45,960 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:45,961 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:45,961 | ^ 2023-09-12T11:08:45,962 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:45,963 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:45,964 | ^~~~~~~~ 2023-09-12T11:08:45,978 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:45,978 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:45,979 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:45,979 | ^ 2023-09-12T11:08:45,980 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:45,980 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:45,981 | ^~~~~~~~ 2023-09-12T11:08:45,984 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:45,985 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:45,985 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:45,986 | ^ 2023-09-12T11:08:45,986 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:45,987 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:45,988 | ^~~~~~~~ 2023-09-12T11:08:46,156 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:46,157 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:46,157 from ./src/formats/rsmiformat.cpp:20: 2023-09-12T11:08:46,158 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:46,159 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:46,160 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:46,160 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:46,161 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:08:46,162 from ./src/formats/rsmiformat.cpp:17: 2023-09-12T11:08:46,162 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:46,163 131 | struct binary_function 2023-09-12T11:08:46,164 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:51,961 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:51,962 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/ccCulpd9.s 2023-09-12T11:08:51,966 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:08:52,430 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/ 2023-09-12T11:08:52,430 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/ 2023-09-12T11:08:52,431 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:08:52,433 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/rxnformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/rxnformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:08:52,437 Using built-in specs. 2023-09-12T11:08:52,438 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:08:52,439 Target: arm-linux-gnueabihf 2023-09-12T11:08:52,439 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 2023-09-12T11:08:52,440 Thread model: posix 2023-09-12T11:08:52,440 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:08:52,441 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:08:52,442 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:52,442 /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/cczdKC1H.s 2023-09-12T11:08:52,451 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:52,452 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:52,453 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:52,453 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:52,454 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:08:52,454 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:08:52,455 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:08:52,455 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:08:52,456 ignoring duplicate directory "/usr/include/" 2023-09-12T11:08:52,456 as it is a non-system directory that duplicates a system directory 2023-09-12T11:08:52,457 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:08:52,457 #include "..." search starts here: 2023-09-12T11:08:52,458 #include <...> search starts here: 2023-09-12T11:08:52,458 /usr/include/eigen3 2023-09-12T11:08:52,459 include 2023-09-12T11:08:52,459 /usr/include/python3.11 2023-09-12T11:08:52,460 /usr/include/c++/12 2023-09-12T11:08:52,460 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:08:52,461 /usr/include/c++/12/backward 2023-09-12T11:08:52,461 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:08:52,462 /usr/local/include 2023-09-12T11:08:52,463 /usr/include/arm-linux-gnueabihf 2023-09-12T11:08:52,463 /usr/include 2023-09-12T11:08:52,464 End of search list. 2023-09-12T11:08:52,465 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:08:52,465 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:08:52,466 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:08:52,467 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:08:52,473 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:08:54,217 In file included from include/openbabel/atom.h:33, 2023-09-12T11:08:54,217 from include/openbabel/mol.h:43, 2023-09-12T11:08:54,218 from ./src/formats/rxnformat.cpp:20: 2023-09-12T11:08:54,219 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:08:54,220 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:08:54,220 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:08:54,221 | ^ 2023-09-12T11:08:54,221 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:08:54,222 37 | # define UNUSED(x) x 2023-09-12T11:08:54,223 | ^ 2023-09-12T11:08:54,989 In file included from include/openbabel/mol.h:52: 2023-09-12T11:08:54,989 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:54,990 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:54,991 862 | {return new OBVibrationData(*this);} 2023-09-12T11:08:54,991 | ^ 2023-09-12T11:08:54,992 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:08:54,993 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:08:54,994 | ^~~~~~~~ 2023-09-12T11:08:54,996 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:54,996 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:54,997 907 | {return new OBDOSData(*this);} 2023-09-12T11:08:54,997 | ^ 2023-09-12T11:08:54,998 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:08:54,998 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:08:54,999 | ^~~~~~~~ 2023-09-12T11:08:55,015 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:55,016 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:55,017 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:08:55,017 | ^ 2023-09-12T11:08:55,018 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:08:55,019 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:08:55,019 | ^~~~~~~~ 2023-09-12T11:08:55,023 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:08:55,024 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:08:55,024 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:08:55,025 | ^ 2023-09-12T11:08:55,026 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:08:55,027 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:08:55,027 | ^~~~~~~~ 2023-09-12T11:08:55,202 In file included from include/openbabel/format.h:22, 2023-09-12T11:08:55,202 from include/openbabel/obconversion.h:37, 2023-09-12T11:08:55,203 from ./src/formats/rxnformat.cpp:21: 2023-09-12T11:08:55,204 include/openbabel/plugin.h: At global scope: 2023-09-12T11:08:55,204 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:08:55,205 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:08:55,206 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:55,207 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:08:55,208 from ./src/formats/rxnformat.cpp:17: 2023-09-12T11:08:55,209 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:08:55,209 131 | struct binary_function 2023-09-12T11:08:55,210 | ^~~~~~~~~~~~~~~ 2023-09-12T11:08:55,564 ./src/formats/rxnformat.cpp: In member function ‘virtual bool OpenBabel::RXNFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:08:55,565 ./src/formats/rxnformat.cpp:228:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:08:55,565 228 | for(i=0;iNumReactants();i++) 2023-09-12T11:08:55,566 | ~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:55,566 ./src/formats/rxnformat.cpp:235:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T11:08:55,567 235 | for(i=0;iNumProducts();i++) 2023-09-12T11:08:55,568 | ~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:08:59,846 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:08:59,846 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/cczdKC1H.s 2023-09-12T11:08:59,851 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:00,191 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/ 2023-09-12T11:09:00,191 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/ 2023-09-12T11:09:00,192 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/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.' 2023-09-12T11:09:00,194 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 2023-09-12T11:09:00,198 Using built-in specs. 2023-09-12T11:09:00,199 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:00,199 Target: arm-linux-gnueabihf 2023-09-12T11:09:00,200 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 2023-09-12T11:09:00,201 Thread model: posix 2023-09-12T11:09:00,201 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:00,202 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:00,202 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:00,203 /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/ccM1K1y5.s 2023-09-12T11:09:00,211 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:00,212 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:00,213 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:00,213 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:00,214 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:00,214 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:00,215 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:00,216 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:00,216 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:00,217 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:00,217 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:00,218 #include "..." search starts here: 2023-09-12T11:09:00,218 #include <...> search starts here: 2023-09-12T11:09:00,219 /usr/include/eigen3 2023-09-12T11:09:00,220 include 2023-09-12T11:09:00,220 /usr/include/python3.11 2023-09-12T11:09:00,221 /usr/include/c++/12 2023-09-12T11:09:00,221 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:00,222 /usr/include/c++/12/backward 2023-09-12T11:09:00,222 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:00,223 /usr/local/include 2023-09-12T11:09:00,224 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:00,224 /usr/include 2023-09-12T11:09:00,225 End of search list. 2023-09-12T11:09:00,226 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:00,226 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 2023-09-12T11:09:00,228 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:00,228 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:00,229 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:01,874 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:01,875 from include/openbabel/mol.h:43, 2023-09-12T11:09:01,876 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:01,876 from ./src/formats/shelxformat.cpp:18: 2023-09-12T11:09:01,877 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:01,877 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:01,878 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:01,878 | ^ 2023-09-12T11:09:01,879 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:01,879 37 | # define UNUSED(x) x 2023-09-12T11:09:01,880 | ^ 2023-09-12T11:09:02,542 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:02,542 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:02,543 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:02,543 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:02,544 | ^ 2023-09-12T11:09:02,545 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:02,546 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:02,546 | ^~~~~~~~ 2023-09-12T11:09:02,547 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:02,548 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:02,549 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:02,550 | ^ 2023-09-12T11:09:02,550 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:02,551 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:02,552 | ^~~~~~~~ 2023-09-12T11:09:02,566 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:02,566 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:02,567 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:02,568 | ^ 2023-09-12T11:09:02,569 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:02,569 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:02,570 | ^~~~~~~~ 2023-09-12T11:09:02,572 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:02,573 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:02,573 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:02,574 | ^ 2023-09-12T11:09:02,574 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:02,575 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:02,575 | ^~~~~~~~ 2023-09-12T11:09:02,744 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:02,745 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:02,745 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:02,746 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:02,747 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:02,747 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:02,748 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:02,748 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:09:02,749 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:09:02,750 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:09:02,751 from /usr/include/c++/12/ios:42, 2023-09-12T11:09:02,751 from /usr/include/c++/12/ostream:38, 2023-09-12T11:09:02,752 from include/openbabel/math/matrix3x3.h:24, 2023-09-12T11:09:02,753 from ./src/formats/shelxformat.cpp:17: 2023-09-12T11:09:02,754 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:02,754 131 | struct binary_function 2023-09-12T11:09:02,755 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:05,460 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:05,460 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/ccM1K1y5.s 2023-09-12T11:09:05,465 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:05,633 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/ 2023-09-12T11:09:05,634 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/ 2023-09-12T11:09:05,635 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:09:05,636 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 2023-09-12T11:09:05,639 Using built-in specs. 2023-09-12T11:09:05,640 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:05,641 Target: arm-linux-gnueabihf 2023-09-12T11:09:05,641 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 2023-09-12T11:09:05,642 Thread model: posix 2023-09-12T11:09:05,642 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:05,643 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:05,643 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:05,644 /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/ccgG8qFt.s 2023-09-12T11:09:05,652 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:05,653 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 2023-09-12T11:09:05,654 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:05,655 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:05,656 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:05,656 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:05,657 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:05,657 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:05,657 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:05,658 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:05,658 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:05,659 #include "..." search starts here: 2023-09-12T11:09:05,659 #include <...> search starts here: 2023-09-12T11:09:05,660 /usr/include/eigen3 2023-09-12T11:09:05,660 include 2023-09-12T11:09:05,660 /usr/include/python3.11 2023-09-12T11:09:05,661 /usr/include/c++/12 2023-09-12T11:09:05,661 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:05,662 /usr/include/c++/12/backward 2023-09-12T11:09:05,662 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:05,663 /usr/local/include 2023-09-12T11:09:05,663 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:05,664 /usr/include 2023-09-12T11:09:05,664 End of search list. 2023-09-12T11:09:05,665 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:05,665 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 2023-09-12T11:09:05,666 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:05,667 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:05,670 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:07,232 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:07,233 from include/openbabel/mol.h:43, 2023-09-12T11:09:07,234 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:07,234 from ./src/formats/siestaformat.cpp:16: 2023-09-12T11:09:07,235 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:07,236 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:07,237 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:07,237 | ^ 2023-09-12T11:09:07,238 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:07,239 37 | # define UNUSED(x) x 2023-09-12T11:09:07,239 | ^ 2023-09-12T11:09:08,000 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:08,001 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:08,002 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:08,002 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:08,003 | ^ 2023-09-12T11:09:08,004 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:08,005 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:08,005 | ^~~~~~~~ 2023-09-12T11:09:08,007 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:08,008 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:08,008 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:08,009 | ^ 2023-09-12T11:09:08,010 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:08,010 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:08,011 | ^~~~~~~~ 2023-09-12T11:09:08,026 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:08,027 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:08,027 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:08,028 | ^ 2023-09-12T11:09:08,028 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:08,029 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:08,030 | ^~~~~~~~ 2023-09-12T11:09:08,033 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:08,033 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:08,034 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:08,035 | ^ 2023-09-12T11:09:08,035 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:08,036 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:08,037 | ^~~~~~~~ 2023-09-12T11:09:08,206 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:08,206 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:08,207 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:08,208 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:08,208 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:08,209 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:08,210 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:08,210 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:08,211 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:08,212 from include/openbabel/mol.h:35: 2023-09-12T11:09:08,212 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:08,213 131 | struct binary_function 2023-09-12T11:09:08,214 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:08,405 ./src/formats/siestaformat.cpp: In member function ‘virtual int OpenBabel::SIESTAFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:09:08,406 ./src/formats/siestaformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:09:08,407 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:09:08,407 | ~~~~^ 2023-09-12T11:09:08,408 ./src/formats/siestaformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:09:08,409 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:09:08,409 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:09:08,470 ./src/formats/siestaformat.cpp: In member function ‘virtual bool OpenBabel::SIESTAFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:08,470 ./src/formats/siestaformat.cpp:82:10: warning: variable ‘coordsAreAngstrom’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:09:08,471 82 | bool coordsAreAngstrom = false; 2023-09-12T11:09:08,471 | ^~~~~~~~~~~~~~~~~ 2023-09-12T11:09:08,472 ./src/formats/siestaformat.cpp:88:12: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 2023-09-12T11:09:08,472 88 | size_t size; 2023-09-12T11:09:08,473 | ^~~~ 2023-09-12T11:09:08,473 ./src/formats/siestaformat.cpp:92:30: warning: unused variable ‘numSpecies’ [-Wunused-variable] 2023-09-12T11:09:08,474 92 | int atomicNum, numAtoms, numSpecies; 2023-09-12T11:09:08,475 | ^~~~~~~~~~ 2023-09-12T11:09:14,307 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:14,308 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/ccgG8qFt.s 2023-09-12T11:09:14,313 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:14,723 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/ 2023-09-12T11:09:14,723 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/ 2023-09-12T11:09:14,724 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/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.' 2023-09-12T11:09:14,725 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 2023-09-12T11:09:14,729 Using built-in specs. 2023-09-12T11:09:14,730 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:14,731 Target: arm-linux-gnueabihf 2023-09-12T11:09:14,731 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 2023-09-12T11:09:14,732 Thread model: posix 2023-09-12T11:09:14,732 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:14,733 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:14,733 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/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/' 2023-09-12T11:09:14,734 /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/ccPUgvmI.s 2023-09-12T11:09:14,742 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:14,743 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 2023-09-12T11:09:14,744 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:14,744 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:14,745 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:14,745 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:14,746 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:14,746 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:14,747 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:14,748 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:14,748 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:14,749 #include "..." search starts here: 2023-09-12T11:09:14,750 #include <...> search starts here: 2023-09-12T11:09:14,750 /usr/include/eigen3 2023-09-12T11:09:14,751 include 2023-09-12T11:09:14,752 /usr/include/python3.11 2023-09-12T11:09:14,752 /usr/include/c++/12 2023-09-12T11:09:14,753 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:14,753 /usr/include/c++/12/backward 2023-09-12T11:09:14,754 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:14,754 /usr/local/include 2023-09-12T11:09:14,755 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:14,755 /usr/include 2023-09-12T11:09:14,756 End of search list. 2023-09-12T11:09:14,756 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:14,757 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 2023-09-12T11:09:14,757 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:14,758 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:14,761 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:16,329 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:16,330 from include/openbabel/mol.h:43, 2023-09-12T11:09:16,330 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:16,331 from ./src/formats/smileyformat.cpp:15: 2023-09-12T11:09:16,331 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:16,332 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:16,332 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:16,333 | ^ 2023-09-12T11:09:16,334 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:16,335 37 | # define UNUSED(x) x 2023-09-12T11:09:16,335 | ^ 2023-09-12T11:09:17,095 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:17,096 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,096 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,097 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:17,098 | ^ 2023-09-12T11:09:17,099 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:17,100 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:17,101 | ^~~~~~~~ 2023-09-12T11:09:17,101 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,102 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,103 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:17,103 | ^ 2023-09-12T11:09:17,104 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:17,105 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:17,105 | ^~~~~~~~ 2023-09-12T11:09:17,119 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,120 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,121 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:17,122 | ^ 2023-09-12T11:09:17,122 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:17,123 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:17,124 | ^~~~~~~~ 2023-09-12T11:09:17,126 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:17,126 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:17,127 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:17,127 | ^ 2023-09-12T11:09:17,128 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:17,129 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:17,129 | ^~~~~~~~ 2023-09-12T11:09:17,297 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:17,298 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:17,299 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:17,300 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:17,300 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:17,301 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:17,302 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:17,303 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:17,303 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:17,304 from include/openbabel/mol.h:35: 2023-09-12T11:09:17,305 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:17,306 131 | struct binary_function 2023-09-12T11:09:17,306 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:17,644 In file included from ./src/formats/smileyformat.cpp:20: 2023-09-12T11:09:17,644 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setChiral(int, Smiley::Chirality, const std::vector&)’: 2023-09-12T11:09:17,645 include/formats/smiley.h:649:24: warning: unused parameter ‘index’ [-Wunused-parameter] 2023-09-12T11:09:17,646 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2023-09-12T11:09:17,646 | ~~~~^~~~~ 2023-09-12T11:09:17,647 include/formats/smiley.h:649:41: warning: unused parameter ‘chirality’ [-Wunused-parameter] 2023-09-12T11:09:17,648 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2023-09-12T11:09:17,648 | ~~~~~~~~~~^~~~~~~~~ 2023-09-12T11:09:17,649 include/formats/smiley.h:649:76: warning: unused parameter ‘chiralNbrs’ [-Wunused-parameter] 2023-09-12T11:09:17,650 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2023-09-12T11:09:17,651 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2023-09-12T11:09:17,652 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addAtom(int, bool, int, int, int, int)’: 2023-09-12T11:09:17,653 include/formats/smiley.h:655:22: warning: unused parameter ‘element’ [-Wunused-parameter] 2023-09-12T11:09:17,653 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:09:17,654 | ~~~~^~~~~~~ 2023-09-12T11:09:17,654 include/formats/smiley.h:655:36: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2023-09-12T11:09:17,655 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:09:17,655 | ~~~~~^~~~~~~~ 2023-09-12T11:09:17,656 include/formats/smiley.h:655:50: warning: unused parameter ‘isotope’ [-Wunused-parameter] 2023-09-12T11:09:17,657 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:09:17,657 | ~~~~^~~~~~~ 2023-09-12T11:09:17,658 include/formats/smiley.h:655:63: warning: unused parameter ‘hCount’ [-Wunused-parameter] 2023-09-12T11:09:17,658 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:09:17,659 | ~~~~^~~~~~ 2023-09-12T11:09:17,659 include/formats/smiley.h:655:75: warning: unused parameter ‘charge’ [-Wunused-parameter] 2023-09-12T11:09:17,660 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:09:17,661 | ~~~~^~~~~~ 2023-09-12T11:09:17,662 include/formats/smiley.h:655:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2023-09-12T11:09:17,662 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2023-09-12T11:09:17,663 | ~~~~^~~~~~~~~ 2023-09-12T11:09:17,664 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addBond(int, int, int, bool, bool)’: 2023-09-12T11:09:17,665 include/formats/smiley.h:659:22: warning: unused parameter ‘source’ [-Wunused-parameter] 2023-09-12T11:09:17,666 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:09:17,666 | ~~~~^~~~~~ 2023-09-12T11:09:17,667 include/formats/smiley.h:659:34: warning: unused parameter ‘target’ [-Wunused-parameter] 2023-09-12T11:09:17,668 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:09:17,669 | ~~~~^~~~~~ 2023-09-12T11:09:17,669 include/formats/smiley.h:659:46: warning: unused parameter ‘order’ [-Wunused-parameter] 2023-09-12T11:09:17,670 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:09:17,671 | ~~~~^~~~~ 2023-09-12T11:09:17,672 include/formats/smiley.h:659:58: warning: unused parameter ‘isUp’ [-Wunused-parameter] 2023-09-12T11:09:17,672 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:09:17,673 | ~~~~~^~~~ 2023-09-12T11:09:17,674 include/formats/smiley.h:659:69: warning: unused parameter ‘isDown’ [-Wunused-parameter] 2023-09-12T11:09:17,675 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2023-09-12T11:09:17,675 | ~~~~~^~~~~~ 2023-09-12T11:09:17,676 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::operation(int)’: 2023-09-12T11:09:17,677 include/formats/smiley.h:667:24: warning: unused parameter ‘type’ [-Wunused-parameter] 2023-09-12T11:09:17,678 667 | void operation(int type) {} 2023-09-12T11:09:17,679 | ~~~~^~~~ 2023-09-12T11:09:17,679 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addOrganicSubsetAtom(int, bool)’: 2023-09-12T11:09:17,680 include/formats/smiley.h:671:35: warning: unused parameter ‘element’ [-Wunused-parameter] 2023-09-12T11:09:17,680 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2023-09-12T11:09:17,681 | ~~~~^~~~~~~ 2023-09-12T11:09:17,681 include/formats/smiley.h:671:49: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2023-09-12T11:09:17,682 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2023-09-12T11:09:17,683 | ~~~~~^~~~~~~~ 2023-09-12T11:09:17,683 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::atomPrimitive(int, int)’: 2023-09-12T11:09:17,684 include/formats/smiley.h:675:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2023-09-12T11:09:17,684 675 | void atomPrimitive(int type, int value) {} 2023-09-12T11:09:17,685 | ~~~~^~~~ 2023-09-12T11:09:17,685 include/formats/smiley.h:675:38: warning: unused parameter ‘value’ [-Wunused-parameter] 2023-09-12T11:09:17,686 675 | void atomPrimitive(int type, int value) {} 2023-09-12T11:09:17,686 | ~~~~^~~~~ 2023-09-12T11:09:17,687 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::bondPrimitive(int)’: 2023-09-12T11:09:17,688 include/formats/smiley.h:680:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2023-09-12T11:09:17,688 680 | void bondPrimitive(int type) {} 2023-09-12T11:09:17,689 | ~~~~^~~~ 2023-09-12T11:09:17,690 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setPrevious(int)’: 2023-09-12T11:09:17,691 include/formats/smiley.h:685:26: warning: unused parameter ‘index’ [-Wunused-parameter] 2023-09-12T11:09:17,691 685 | void setPrevious(int index) {} 2023-09-12T11:09:17,692 | ~~~~^~~~~ 2023-09-12T11:09:17,693 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::startRingBond(int)’: 2023-09-12T11:09:17,694 include/formats/smiley.h:689:28: warning: unused parameter ‘number’ [-Wunused-parameter] 2023-09-12T11:09:17,694 689 | void startRingBond(int number) {} 2023-09-12T11:09:17,695 | ~~~~^~~~~~ 2023-09-12T11:09:17,696 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::endRingBond(int, int)’: 2023-09-12T11:09:17,697 include/formats/smiley.h:693:26: warning: unused parameter ‘number’ [-Wunused-parameter] 2023-09-12T11:09:17,697 693 | void endRingBond(int number, int index) {} 2023-09-12T11:09:17,698 | ~~~~^~~~~~ 2023-09-12T11:09:17,698 include/formats/smiley.h:693:38: warning: unused parameter ‘index’ [-Wunused-parameter] 2023-09-12T11:09:17,699 693 | void endRingBond(int number, int index) {} 2023-09-12T11:09:17,700 | ~~~~^~~~~ 2023-09-12T11:09:17,770 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::addAtom(int, bool, int, int, int, int)’: 2023-09-12T11:09:17,770 ./src/formats/smileyformat.cpp:58:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2023-09-12T11:09:17,771 58 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) 2023-09-12T11:09:17,772 | ~~~~^~~~~~~~~ 2023-09-12T11:09:17,774 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::setChiral(int, Smiley::Chirality, const std::vector&)’: 2023-09-12T11:09:17,775 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘NotChiral’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,775 153 | switch (chirality) { 2023-09-12T11:09:17,776 | ^ 2023-09-12T11:09:17,777 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH1’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,777 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH2’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,778 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL1’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,778 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL2’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,779 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP1’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,780 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP2’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,780 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP3’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,781 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB1’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,781 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB2’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,782 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB3’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,783 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB4’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,783 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB5’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,784 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB6’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,785 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB7’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,785 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB8’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,786 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB9’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,787 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB10’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,787 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB11’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,788 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB12’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,789 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB13’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,790 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB14’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,790 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB15’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,791 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB16’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,792 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB17’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,792 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB18’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,793 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB19’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,794 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB20’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,794 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH1’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,795 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH2’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,796 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH3’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,797 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH4’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,797 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH5’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,798 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH6’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,798 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH7’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,799 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH8’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,799 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH9’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,800 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH10’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,800 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH11’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,801 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH12’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,802 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH13’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,802 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH14’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,803 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH15’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,803 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH16’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,804 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH17’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,805 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH18’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,806 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH19’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,807 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH20’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,807 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH21’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,808 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH22’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,809 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH23’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,809 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH24’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,810 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH25’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,811 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH26’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,811 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH27’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,812 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH28’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,813 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH29’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,813 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH30’ not handled in switch [-Wswitch] 2023-09-12T11:09:17,838 ./src/formats/smileyformat.cpp: In member function ‘bool OpenBabel::SmileyFormat::AssignNbrAtoms(const std::vector&, OpenBabel::OBAtom*, long unsigned int&, long unsigned int&)’: 2023-09-12T11:09:17,839 ./src/formats/smileyformat.cpp:457:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:09:17,840 457 | aboveId = above ? above->GetId() : OBStereo::ImplicitRef; 2023-09-12T11:09:17,840 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:17,841 ./src/formats/smileyformat.cpp:458:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2023-09-12T11:09:17,841 458 | belowId = below ? below->GetId() : OBStereo::ImplicitRef; 2023-09-12T11:09:17,842 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:18,491 include/formats/smiley.h: In instantiation of ‘void Smiley::Parser::processStereochemistry() [with Callback = OpenBabel::OpenBabelCallback]’: 2023-09-12T11:09:18,492 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]’ 2023-09-12T11:09:18,492 ./src/formats/smileyformat.cpp:365:19: required from here 2023-09-12T11:09:18,493 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] 2023-09-12T11:09:18,493 2642 | if (m_chiralInfo[i].nbrs.size() != expectedValence && m_exceptions & InvalidChiralValence) 2023-09-12T11:09:18,494 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:19,123 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]’: 2023-09-12T11:09:19,124 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]’ 2023-09-12T11:09:19,125 include/formats/smiley.h:2429:11: required from ‘void Smiley::Parser::parseRingBond() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:09:19,125 include/formats/smiley.h:2507:13: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:09:19,126 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]’ 2023-09-12T11:09:19,127 ./src/formats/smileyformat.cpp:365:19: required from here 2023-09-12T11:09:19,128 include/formats/smiley.h:986:14: warning: ‘Smiley::Parser::RingBondInfo::isExplicit’ will be initialized after [-Wreorder] 2023-09-12T11:09:19,128 986 | bool isExplicit; 2023-09-12T11:09:19,129 | ^~~~~~~~~~ 2023-09-12T11:09:19,130 include/formats/smiley.h:981:21: warning: ‘std::size_t Smiley::Parser::RingBondInfo::pos’ [-Wreorder] 2023-09-12T11:09:19,131 981 | std::size_t pos; 2023-09-12T11:09:19,131 | ^~~ 2023-09-12T11:09:19,132 include/formats/smiley.h:974:9: warning: when initialized here [-Wreorder] 2023-09-12T11:09:19,133 974 | RingBondInfo(int number_, int order_, bool isUp_, bool isDown_, 2023-09-12T11:09:19,134 | ^~~~~~~~~~~~ 2023-09-12T11:09:19,203 include/formats/smiley.h: In instantiation of ‘bool Smiley::Parser::parseCharNumber(char, int, int&, bool, bool) [with Callback = OpenBabel::OpenBabelCallback]’: 2023-09-12T11:09:19,204 include/formats/smiley.h:1988:15: required from ‘void Smiley::Parser::parseAtomExpr() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:09:19,204 include/formats/smiley.h:2092:11: required from ‘void Smiley::Parser::parseBracketAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:09:19,205 include/formats/smiley.h:2217:13: required from ‘bool Smiley::Parser::parseAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:09:19,206 include/formats/smiley.h:2495:16: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2023-09-12T11:09:19,207 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]’ 2023-09-12T11:09:19,207 ./src/formats/smileyformat.cpp:365:19: required from here 2023-09-12T11:09:19,208 include/formats/smiley.h:1774:37: warning: unused parameter ‘noDefault’ [-Wunused-parameter] 2023-09-12T11:09:19,208 1774 | bool firstPrimitive, bool noDefault = false) 2023-09-12T11:09:19,209 | ~~~~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:09:27,378 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/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/' 2023-09-12T11:09:27,379 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/ccPUgvmI.s 2023-09-12T11:09:27,387 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:28,080 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/ 2023-09-12T11:09:28,081 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/ 2023-09-12T11:09:28,081 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:09:28,084 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 2023-09-12T11:09:28,089 Using built-in specs. 2023-09-12T11:09:28,090 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:28,091 Target: arm-linux-gnueabihf 2023-09-12T11:09:28,091 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 2023-09-12T11:09:28,092 Thread model: posix 2023-09-12T11:09:28,093 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:28,093 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:28,093 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:28,094 /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/cc3r1SM8.s 2023-09-12T11:09:28,103 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:28,103 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:28,104 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:28,105 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:28,105 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:28,106 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:28,107 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:28,107 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:28,108 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:28,108 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:28,109 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:28,109 #include "..." search starts here: 2023-09-12T11:09:28,110 #include <...> search starts here: 2023-09-12T11:09:28,111 /usr/include/eigen3 2023-09-12T11:09:28,111 include 2023-09-12T11:09:28,112 /usr/include/python3.11 2023-09-12T11:09:28,112 /usr/include/c++/12 2023-09-12T11:09:28,113 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:28,114 /usr/include/c++/12/backward 2023-09-12T11:09:28,114 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:28,115 /usr/local/include 2023-09-12T11:09:28,115 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:28,116 /usr/include 2023-09-12T11:09:28,117 End of search list. 2023-09-12T11:09:28,117 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:28,118 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:28,119 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:28,120 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:28,122 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:29,680 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:29,680 from include/openbabel/mol.h:43, 2023-09-12T11:09:29,681 from ./src/formats/stlformat.cpp:28: 2023-09-12T11:09:29,681 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:29,682 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:29,682 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:29,683 | ^ 2023-09-12T11:09:29,684 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:29,684 37 | # define UNUSED(x) x 2023-09-12T11:09:29,685 | ^ 2023-09-12T11:09:30,445 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:30,446 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:30,447 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:30,447 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:30,448 | ^ 2023-09-12T11:09:30,448 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:30,449 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:30,450 | ^~~~~~~~ 2023-09-12T11:09:30,451 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:30,451 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:30,452 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:30,453 | ^ 2023-09-12T11:09:30,453 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:30,454 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:30,455 | ^~~~~~~~ 2023-09-12T11:09:30,470 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:30,470 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:30,471 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:30,472 | ^ 2023-09-12T11:09:30,473 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:30,473 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:30,474 | ^~~~~~~~ 2023-09-12T11:09:30,476 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:30,477 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:30,477 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:30,478 | ^ 2023-09-12T11:09:30,478 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:30,479 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:30,479 | ^~~~~~~~ 2023-09-12T11:09:30,648 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:30,649 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:30,650 from ./src/formats/stlformat.cpp:29: 2023-09-12T11:09:30,650 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:30,651 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:30,651 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:30,652 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:30,652 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:30,653 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:30,654 from include/openbabel/mol.h:35: 2023-09-12T11:09:30,654 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:30,655 131 | struct binary_function 2023-09-12T11:09:30,656 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:30,847 ./src/formats/stlformat.cpp: In member function ‘virtual int OpenBabel::STLFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:09:30,848 ./src/formats/stlformat.cpp:95:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:09:30,848 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:09:30,849 | ~~~~^ 2023-09-12T11:09:30,850 ./src/formats/stlformat.cpp:95:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:09:30,851 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2023-09-12T11:09:30,851 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:09:30,865 ./src/formats/stlformat.cpp: In function ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’: 2023-09-12T11:09:30,865 ./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] 2023-09-12T11:09:30,866 149 | for( int i=0 ; i < points.size()-2; i++ ) { 2023-09-12T11:09:30,867 | ~~^~~~~~~~~~~~~~~~~ 2023-09-12T11:09:33,126 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:09:33,127 /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]’: 2023-09-12T11:09:33,127 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:33,128 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:09:33,128 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:33,214 /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]’: 2023-09-12T11:09:33,214 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:09:33,330 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:09:33,331 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, 2023-09-12T11:09:33,331 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:144:25: 2023-09-12T11:09:33,332 /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 2023-09-12T11:09:33,333 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:33,333 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:33,334 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:09:33,334 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, 2023-09-12T11:09:33,335 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:145:25: 2023-09-12T11:09:33,336 /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 2023-09-12T11:09:33,336 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:33,337 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:33,337 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::Triangle}; _Tp = OpenBabel::Triangle; _Alloc = std::allocator]’, 2023-09-12T11:09:33,338 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, 2023-09-12T11:09:33,338 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:152:28: 2023-09-12T11:09:33,339 /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 2023-09-12T11:09:33,340 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:33,340 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:33,341 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::Triangle}; _Tp = OpenBabel::Triangle; _Alloc = std::allocator]’, 2023-09-12T11:09:33,341 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, 2023-09-12T11:09:33,342 inlined from ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’ at ./src/formats/stlformat.cpp:155:28: 2023-09-12T11:09:33,343 /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 2023-09-12T11:09:33,343 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:09:33,344 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:09:33,693 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:33,693 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/cc3r1SM8.s 2023-09-12T11:09:33,698 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:33,874 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/ 2023-09-12T11:09:33,875 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/ 2023-09-12T11:09:33,876 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:09:33,876 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 2023-09-12T11:09:33,880 Using built-in specs. 2023-09-12T11:09:33,881 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:33,881 Target: arm-linux-gnueabihf 2023-09-12T11:09:33,882 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 2023-09-12T11:09:33,883 Thread model: posix 2023-09-12T11:09:33,883 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:33,884 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:33,884 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:33,885 /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/cc9aF2ZM.s 2023-09-12T11:09:33,893 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:33,894 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:33,895 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:33,895 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:33,896 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:33,896 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:33,897 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:33,897 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:33,898 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:33,899 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:33,899 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:33,900 #include "..." search starts here: 2023-09-12T11:09:33,901 #include <...> search starts here: 2023-09-12T11:09:33,901 /usr/include/eigen3 2023-09-12T11:09:33,902 include 2023-09-12T11:09:33,902 /usr/include/python3.11 2023-09-12T11:09:33,903 /usr/include/c++/12 2023-09-12T11:09:33,903 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:33,904 /usr/include/c++/12/backward 2023-09-12T11:09:33,904 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:33,905 /usr/local/include 2023-09-12T11:09:33,906 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:33,906 /usr/include 2023-09-12T11:09:33,907 End of search list. 2023-09-12T11:09:33,907 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:33,908 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 2023-09-12T11:09:33,909 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:33,910 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:33,913 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:35,531 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:35,531 from include/openbabel/mol.h:43, 2023-09-12T11:09:35,532 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:35,532 from ./src/formats/svgformat.cpp:15: 2023-09-12T11:09:35,533 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:35,533 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:35,534 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:35,534 | ^ 2023-09-12T11:09:35,535 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:35,535 37 | # define UNUSED(x) x 2023-09-12T11:09:35,536 | ^ 2023-09-12T11:09:36,304 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:36,305 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:36,306 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:36,306 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:36,307 | ^ 2023-09-12T11:09:36,307 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:36,308 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:36,309 | ^~~~~~~~ 2023-09-12T11:09:36,310 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:36,311 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:36,312 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:36,313 | ^ 2023-09-12T11:09:36,313 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:36,314 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:36,315 | ^~~~~~~~ 2023-09-12T11:09:36,330 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:36,330 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:36,331 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:36,332 | ^ 2023-09-12T11:09:36,333 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:36,333 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:36,334 | ^~~~~~~~ 2023-09-12T11:09:36,337 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:36,337 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:36,339 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:36,339 | ^ 2023-09-12T11:09:36,340 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:36,340 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:36,341 | ^~~~~~~~ 2023-09-12T11:09:36,509 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:36,510 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:36,510 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:36,511 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:36,511 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:36,512 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:36,512 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:36,513 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:36,514 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:36,514 from include/openbabel/mol.h:35: 2023-09-12T11:09:36,515 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:36,515 131 | struct binary_function 2023-09-12T11:09:36,516 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:36,978 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteChemObject(OpenBabel::OBConversion*)’: 2023-09-12T11:09:36,979 ./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] 2023-09-12T11:09:36,980 222 | bool nomore = _nmax && (_objects.size()==_nmax); 2023-09-12T11:09:36,980 | ~~~~~~~~~~~~~~~^~~~~~~ 2023-09-12T11:09:36,984 ./src/formats/svgformat.cpp:244:18: warning: unused variable ‘n’ [-Wunused-variable] 2023-09-12T11:09:36,985 244 | unsigned int n=0; 2023-09-12T11:09:36,985 | ^ 2023-09-12T11:09:36,987 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:36,987 ./src/formats/svgformat.cpp:269:8: warning: unused variable ‘ret’ [-Wunused-variable] 2023-09-12T11:09:36,988 269 | bool ret = WriteSVG(pConv,_objects); 2023-09-12T11:09:36,989 | ^~~ 2023-09-12T11:09:42,120 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:42,120 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/cc9aF2ZM.s 2023-09-12T11:09:42,125 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:42,484 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/ 2023-09-12T11:09:42,485 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/ 2023-09-12T11:09:42,485 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:09:42,487 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 2023-09-12T11:09:42,491 Using built-in specs. 2023-09-12T11:09:42,492 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:42,492 Target: arm-linux-gnueabihf 2023-09-12T11:09:42,493 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 2023-09-12T11:09:42,493 Thread model: posix 2023-09-12T11:09:42,494 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:42,494 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:42,495 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:42,495 /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/ccXxarMs.s 2023-09-12T11:09:42,504 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:42,505 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:42,506 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:42,506 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:42,507 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:42,507 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:42,507 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:42,508 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:42,508 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:42,509 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:42,509 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:42,510 #include "..." search starts here: 2023-09-12T11:09:42,510 #include <...> search starts here: 2023-09-12T11:09:42,511 /usr/include/eigen3 2023-09-12T11:09:42,511 include 2023-09-12T11:09:42,512 /usr/include/python3.11 2023-09-12T11:09:42,512 /usr/include/c++/12 2023-09-12T11:09:42,513 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:42,513 /usr/include/c++/12/backward 2023-09-12T11:09:42,514 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:42,515 /usr/local/include 2023-09-12T11:09:42,515 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:42,516 /usr/include 2023-09-12T11:09:42,517 End of search list. 2023-09-12T11:09:42,518 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:42,518 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:42,519 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:42,520 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:42,522 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:43,942 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:43,943 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:43,943 from ./src/formats/textformat.cpp:14: 2023-09-12T11:09:43,944 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:43,945 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:43,946 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:43,946 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:09:43,947 from /usr/include/c++/12/bits/locale_classes.h:40, 2023-09-12T11:09:43,948 from /usr/include/c++/12/bits/ios_base.h:41, 2023-09-12T11:09:43,948 from /usr/include/c++/12/ios:42, 2023-09-12T11:09:43,949 from /usr/include/c++/12/ostream:38, 2023-09-12T11:09:43,950 from /usr/include/c++/12/iostream:39, 2023-09-12T11:09:43,950 from include/openbabel/obconversion.h:24: 2023-09-12T11:09:43,951 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:43,952 131 | struct binary_function 2023-09-12T11:09:43,953 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:44,089 In file included from include/openbabel/text.h:23, 2023-09-12T11:09:44,090 from ./src/formats/textformat.cpp:15: 2023-09-12T11:09:44,091 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:44,092 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:44,092 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:44,093 | ^ 2023-09-12T11:09:44,093 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:44,094 37 | # define UNUSED(x) x 2023-09-12T11:09:44,094 | ^ 2023-09-12T11:09:45,425 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:45,425 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/ccXxarMs.s 2023-09-12T11:09:45,430 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:45,568 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/ 2023-09-12T11:09:45,569 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/ 2023-09-12T11:09:45,569 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:09:45,570 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 2023-09-12T11:09:45,574 Using built-in specs. 2023-09-12T11:09:45,575 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:45,575 Target: arm-linux-gnueabihf 2023-09-12T11:09:45,576 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 2023-09-12T11:09:45,576 Thread model: posix 2023-09-12T11:09:45,577 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:45,578 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:45,578 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:09:45,579 /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/ccCwuNgY.s 2023-09-12T11:09:45,587 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:45,587 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 2023-09-12T11:09:45,588 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:45,589 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:45,590 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:45,590 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:45,591 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:45,592 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:45,592 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:45,593 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:45,593 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:45,594 #include "..." search starts here: 2023-09-12T11:09:45,595 #include <...> search starts here: 2023-09-12T11:09:45,595 /usr/include/eigen3 2023-09-12T11:09:45,596 include 2023-09-12T11:09:45,596 /usr/include/python3.11 2023-09-12T11:09:45,597 /usr/include/c++/12 2023-09-12T11:09:45,597 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:45,598 /usr/include/c++/12/backward 2023-09-12T11:09:45,598 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:45,599 /usr/local/include 2023-09-12T11:09:45,599 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:45,600 /usr/include 2023-09-12T11:09:45,601 End of search list. 2023-09-12T11:09:45,601 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:45,602 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:45,603 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:45,604 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:45,604 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:47,284 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:47,284 from include/openbabel/mol.h:43, 2023-09-12T11:09:47,285 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:47,286 from ./src/formats/thermoformat.cpp:19: 2023-09-12T11:09:47,286 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:47,287 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:47,287 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:47,288 | ^ 2023-09-12T11:09:47,288 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:47,289 37 | # define UNUSED(x) x 2023-09-12T11:09:47,289 | ^ 2023-09-12T11:09:48,053 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:48,053 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:48,054 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:48,055 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:48,055 | ^ 2023-09-12T11:09:48,056 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:48,057 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:48,058 | ^~~~~~~~ 2023-09-12T11:09:48,058 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:48,059 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:48,060 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:48,061 | ^ 2023-09-12T11:09:48,061 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:48,062 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:48,063 | ^~~~~~~~ 2023-09-12T11:09:48,077 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:48,078 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:48,079 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:48,079 | ^ 2023-09-12T11:09:48,080 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:48,081 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:48,081 | ^~~~~~~~ 2023-09-12T11:09:48,084 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:48,084 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:48,086 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:48,086 | ^ 2023-09-12T11:09:48,087 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:48,087 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:48,088 | ^~~~~~~~ 2023-09-12T11:09:48,256 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:48,257 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:48,257 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:48,258 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:48,258 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:48,259 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:48,260 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:48,260 In file included from /usr/include/c++/12/string:48, 2023-09-12T11:09:48,261 from ./src/formats/thermoformat.cpp:17: 2023-09-12T11:09:48,262 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:48,262 131 | struct binary_function 2023-09-12T11:09:48,263 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:48,475 In file included from ./src/formats/thermoformat.cpp:20: 2023-09-12T11:09:48,476 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:48,476 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T11:09:48,477 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2023-09-12T11:09:48,478 | ~~~~~~~~^~~~~~ 2023-09-12T11:09:48,497 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:48,497 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2023-09-12T11:09:48,498 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2023-09-12T11:09:48,499 | ~~~~~~~~^~~~~~ 2023-09-12T11:09:52,029 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/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/' 2023-09-12T11:09:52,030 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/ccCwuNgY.s 2023-09-12T11:09:52,034 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:52,280 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/ 2023-09-12T11:09:52,281 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/ 2023-09-12T11:09:52,282 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:09:52,283 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 2023-09-12T11:09:52,287 Using built-in specs. 2023-09-12T11:09:52,288 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:52,288 Target: arm-linux-gnueabihf 2023-09-12T11:09:52,288 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 2023-09-12T11:09:52,289 Thread model: posix 2023-09-12T11:09:52,289 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:52,290 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:52,291 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/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/' 2023-09-12T11:09:52,291 /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/cc5X27Mw.s 2023-09-12T11:09:52,300 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:52,301 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:52,302 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:52,302 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:52,303 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:52,303 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:52,303 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:52,304 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:52,304 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:52,305 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:52,305 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:52,306 #include "..." search starts here: 2023-09-12T11:09:52,306 #include <...> search starts here: 2023-09-12T11:09:52,306 /usr/include/eigen3 2023-09-12T11:09:52,307 include 2023-09-12T11:09:52,307 /usr/include/python3.11 2023-09-12T11:09:52,308 /usr/include/c++/12 2023-09-12T11:09:52,308 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:52,309 /usr/include/c++/12/backward 2023-09-12T11:09:52,309 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:52,310 /usr/local/include 2023-09-12T11:09:52,310 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:52,310 /usr/include 2023-09-12T11:09:52,311 End of search list. 2023-09-12T11:09:52,312 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:52,312 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:52,314 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:52,314 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:52,318 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:53,921 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:53,921 from include/openbabel/mol.h:43, 2023-09-12T11:09:53,922 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:53,923 from ./src/formats/tinkerformat.cpp:17: 2023-09-12T11:09:53,924 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:53,924 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:53,925 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:53,926 | ^ 2023-09-12T11:09:53,927 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:53,927 37 | # define UNUSED(x) x 2023-09-12T11:09:53,928 | ^ 2023-09-12T11:09:54,687 In file included from include/openbabel/mol.h:52: 2023-09-12T11:09:54,687 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:54,688 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:54,689 862 | {return new OBVibrationData(*this);} 2023-09-12T11:09:54,689 | ^ 2023-09-12T11:09:54,690 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:09:54,691 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:09:54,692 | ^~~~~~~~ 2023-09-12T11:09:54,693 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:54,693 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:54,694 907 | {return new OBDOSData(*this);} 2023-09-12T11:09:54,694 | ^ 2023-09-12T11:09:54,695 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:09:54,695 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:09:54,696 | ^~~~~~~~ 2023-09-12T11:09:54,711 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:54,711 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:54,712 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:09:54,713 | ^ 2023-09-12T11:09:54,713 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:09:54,714 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:09:54,714 | ^~~~~~~~ 2023-09-12T11:09:54,717 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:09:54,718 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:09:54,719 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:09:54,719 | ^ 2023-09-12T11:09:54,720 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:09:54,721 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:09:54,722 | ^~~~~~~~ 2023-09-12T11:09:54,890 In file included from include/openbabel/format.h:22, 2023-09-12T11:09:54,890 from include/openbabel/obconversion.h:37, 2023-09-12T11:09:54,891 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:09:54,892 include/openbabel/plugin.h: At global scope: 2023-09-12T11:09:54,892 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:09:54,893 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:09:54,893 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:54,894 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:09:54,895 from /usr/include/c++/12/vector:66, 2023-09-12T11:09:54,896 from include/openbabel/mol.h:35: 2023-09-12T11:09:54,896 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:09:54,897 131 | struct binary_function 2023-09-12T11:09:54,898 | ^~~~~~~~~~~~~~~ 2023-09-12T11:09:55,171 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2023-09-12T11:09:55,172 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,173 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,173 | ^ 2023-09-12T11:09:55,174 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,174 37 | # define UNUSED(x) x 2023-09-12T11:09:55,175 | ^ 2023-09-12T11:09:55,176 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2023-09-12T11:09:55,176 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,177 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,177 | ^ 2023-09-12T11:09:55,178 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,178 37 | # define UNUSED(x) x 2023-09-12T11:09:55,179 | ^ 2023-09-12T11:09:55,180 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2023-09-12T11:09:55,180 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,181 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,181 | ^ 2023-09-12T11:09:55,182 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,183 37 | # define UNUSED(x) x 2023-09-12T11:09:55,184 | ^ 2023-09-12T11:09:55,185 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2023-09-12T11:09:55,185 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,186 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,187 | ^ 2023-09-12T11:09:55,188 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,188 37 | # define UNUSED(x) x 2023-09-12T11:09:55,189 | ^ 2023-09-12T11:09:55,190 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2023-09-12T11:09:55,190 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,191 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,192 | ^ 2023-09-12T11:09:55,192 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,193 37 | # define UNUSED(x) x 2023-09-12T11:09:55,194 | ^ 2023-09-12T11:09:55,194 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2023-09-12T11:09:55,195 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,196 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,196 | ^ 2023-09-12T11:09:55,197 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,198 37 | # define UNUSED(x) x 2023-09-12T11:09:55,199 | ^ 2023-09-12T11:09:55,200 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2023-09-12T11:09:55,200 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,201 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,201 | ^ 2023-09-12T11:09:55,202 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,203 37 | # define UNUSED(x) x 2023-09-12T11:09:55,203 | ^ 2023-09-12T11:09:55,204 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2023-09-12T11:09:55,204 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2023-09-12T11:09:55,205 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2023-09-12T11:09:55,205 | ^ 2023-09-12T11:09:55,206 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:55,207 37 | # define UNUSED(x) x 2023-09-12T11:09:55,207 | ^ 2023-09-12T11:09:55,208 ./src/formats/tinkerformat.cpp: In member function ‘virtual bool OpenBabel::TinkerFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:09:55,208 ./src/formats/tinkerformat.cpp:101:9: warning: unused variable ‘atomicNum’ [-Wunused-variable] 2023-09-12T11:09:55,209 101 | int atomicNum; 2023-09-12T11:09:55,209 | ^~~~~~~~~ 2023-09-12T11:09:55,211 ./src/formats/tinkerformat.cpp: In function ‘int OpenBabel::SetMM3Type(OBAtom*)’: 2023-09-12T11:09:55,211 ./src/formats/tinkerformat.cpp:377:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:09:55,212 377 | if (b->GetHyb() == 2) // S=C 2023-09-12T11:09:55,213 | ^~ 2023-09-12T11:09:55,213 ./src/formats/tinkerformat.cpp:378:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:09:55,214 378 | countNeighborC++; break; 2023-09-12T11:09:55,215 | ^~~~~ 2023-09-12T11:09:55,216 ./src/formats/tinkerformat.cpp:220:17: warning: unused variable ‘c’ [-Wunused-variable] 2023-09-12T11:09:55,217 220 | OBAtom *b, *c; // neighbors 2023-09-12T11:09:55,217 | ^ 2023-09-12T11:09:58,123 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/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/' 2023-09-12T11:09:58,124 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/formats/tinkerformat.o /tmp/cc5X27Mw.s 2023-09-12T11:09:58,129 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:09:58,336 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/ 2023-09-12T11:09:58,336 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/ 2023-09-12T11:09:58,337 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:09:58,338 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 2023-09-12T11:09:58,342 Using built-in specs. 2023-09-12T11:09:58,343 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:09:58,343 Target: arm-linux-gnueabihf 2023-09-12T11:09:58,344 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 2023-09-12T11:09:58,344 Thread model: posix 2023-09-12T11:09:58,345 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:09:58,346 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:09:58,346 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/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/' 2023-09-12T11:09:58,347 /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/ccbLlnj8.s 2023-09-12T11:09:58,355 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:58,355 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:58,357 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:58,357 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:58,358 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:09:58,358 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:09:58,359 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:09:58,359 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:09:58,360 ignoring duplicate directory "/usr/include/" 2023-09-12T11:09:58,360 as it is a non-system directory that duplicates a system directory 2023-09-12T11:09:58,361 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:09:58,361 #include "..." search starts here: 2023-09-12T11:09:58,361 #include <...> search starts here: 2023-09-12T11:09:58,362 /usr/include/eigen3 2023-09-12T11:09:58,362 include 2023-09-12T11:09:58,363 /usr/include/python3.11 2023-09-12T11:09:58,363 /usr/include/c++/12 2023-09-12T11:09:58,364 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:09:58,364 /usr/include/c++/12/backward 2023-09-12T11:09:58,364 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:09:58,365 /usr/local/include 2023-09-12T11:09:58,365 /usr/include/arm-linux-gnueabihf 2023-09-12T11:09:58,366 /usr/include 2023-09-12T11:09:58,366 End of search list. 2023-09-12T11:09:58,367 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:09:58,367 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:09:58,369 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:09:58,369 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:09:58,373 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:09:59,933 In file included from include/openbabel/atom.h:33, 2023-09-12T11:09:59,934 from include/openbabel/mol.h:43, 2023-09-12T11:09:59,934 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:09:59,935 from ./src/formats/titleformat.cpp:19: 2023-09-12T11:09:59,935 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:09:59,936 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:09:59,937 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:09:59,938 | ^ 2023-09-12T11:09:59,938 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:09:59,939 37 | # define UNUSED(x) x 2023-09-12T11:09:59,940 | ^ 2023-09-12T11:10:00,700 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:00,701 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:00,702 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:00,702 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:00,703 | ^ 2023-09-12T11:10:00,704 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:00,705 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:00,705 | ^~~~~~~~ 2023-09-12T11:10:00,706 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:00,707 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:00,708 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:00,708 | ^ 2023-09-12T11:10:00,709 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:00,710 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:00,710 | ^~~~~~~~ 2023-09-12T11:10:00,724 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:00,725 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:00,725 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:00,726 | ^ 2023-09-12T11:10:00,727 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:00,727 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:00,728 | ^~~~~~~~ 2023-09-12T11:10:00,731 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:00,731 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:00,732 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:00,733 | ^ 2023-09-12T11:10:00,734 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:00,735 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:00,735 | ^~~~~~~~ 2023-09-12T11:10:00,903 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:00,904 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:00,905 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:00,906 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:00,906 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:00,907 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:00,908 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:00,908 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:00,909 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:00,910 from include/openbabel/mol.h:35: 2023-09-12T11:10:00,911 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:00,911 131 | struct binary_function 2023-09-12T11:10:00,912 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:03,281 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/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/' 2023-09-12T11:10:03,282 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/ccbLlnj8.s 2023-09-12T11:10:03,287 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:03,420 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/ 2023-09-12T11:10:03,420 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/ 2023-09-12T11:10:03,421 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/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.' 2023-09-12T11:10:03,422 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 2023-09-12T11:10:03,426 Using built-in specs. 2023-09-12T11:10:03,427 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:03,428 Target: arm-linux-gnueabihf 2023-09-12T11:10:03,428 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 2023-09-12T11:10:03,429 Thread model: posix 2023-09-12T11:10:03,429 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:03,430 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:03,431 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:10:03,432 /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/cc5Rp6Ku.s 2023-09-12T11:10:03,440 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:03,441 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 2023-09-12T11:10:03,442 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:03,442 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:03,442 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:03,443 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:03,443 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:03,444 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:03,445 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:03,445 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:03,446 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:03,447 #include "..." search starts here: 2023-09-12T11:10:03,452 #include <...> search starts here: 2023-09-12T11:10:03,453 /usr/include/eigen3 2023-09-12T11:10:03,453 include 2023-09-12T11:10:03,454 /usr/include/python3.11 2023-09-12T11:10:03,455 /usr/include/c++/12 2023-09-12T11:10:03,455 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:03,456 /usr/include/c++/12/backward 2023-09-12T11:10:03,456 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:03,457 /usr/local/include 2023-09-12T11:10:03,458 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:03,458 /usr/include 2023-09-12T11:10:03,459 End of search list. 2023-09-12T11:10:03,460 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:03,460 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:03,461 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:03,462 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:03,462 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:05,017 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:05,018 from include/openbabel/mol.h:43, 2023-09-12T11:10:05,019 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:05,020 from ./src/formats/turbomoleformat.cpp:18: 2023-09-12T11:10:05,020 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:05,021 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:05,021 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:05,022 | ^ 2023-09-12T11:10:05,023 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:05,024 37 | # define UNUSED(x) x 2023-09-12T11:10:05,024 | ^ 2023-09-12T11:10:05,784 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:05,784 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:05,785 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:05,786 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:05,786 | ^ 2023-09-12T11:10:05,787 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:05,787 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:05,788 | ^~~~~~~~ 2023-09-12T11:10:05,789 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:05,790 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:05,791 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:05,791 | ^ 2023-09-12T11:10:05,792 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:05,793 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:05,794 | ^~~~~~~~ 2023-09-12T11:10:05,808 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:05,809 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:05,810 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:05,811 | ^ 2023-09-12T11:10:05,812 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:05,812 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:05,813 | ^~~~~~~~ 2023-09-12T11:10:05,815 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:05,815 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:05,816 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:05,817 | ^ 2023-09-12T11:10:05,818 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:05,818 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:05,819 | ^~~~~~~~ 2023-09-12T11:10:05,989 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:05,989 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:05,990 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:05,990 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:05,991 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:05,991 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:05,992 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:05,993 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:05,993 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:05,994 from include/openbabel/mol.h:35: 2023-09-12T11:10:05,994 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:05,995 131 | struct binary_function 2023-09-12T11:10:05,995 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:08,583 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:10:08,583 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/cc5Rp6Ku.s 2023-09-12T11:10:08,588 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:08,736 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/ 2023-09-12T11:10:08,736 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/ 2023-09-12T11:10:08,737 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/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.' 2023-09-12T11:10:08,738 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 2023-09-12T11:10:08,742 Using built-in specs. 2023-09-12T11:10:08,743 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:08,743 Target: arm-linux-gnueabihf 2023-09-12T11:10:08,744 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 2023-09-12T11:10:08,744 Thread model: posix 2023-09-12T11:10:08,745 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:08,746 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:08,746 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/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/' 2023-09-12T11:10:08,747 /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/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/ccrBWTqR.s 2023-09-12T11:10:08,755 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:08,755 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:08,756 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:08,757 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:08,757 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:08,758 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:08,759 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:08,759 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:08,760 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:08,760 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:08,761 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:08,762 #include "..." search starts here: 2023-09-12T11:10:08,762 #include <...> search starts here: 2023-09-12T11:10:08,763 /usr/include/eigen3 2023-09-12T11:10:08,763 include 2023-09-12T11:10:08,764 /usr/include/python3.11 2023-09-12T11:10:08,765 /usr/include/c++/12 2023-09-12T11:10:08,765 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:08,766 /usr/include/c++/12/backward 2023-09-12T11:10:08,767 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:08,767 /usr/local/include 2023-09-12T11:10:08,768 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:08,769 /usr/include 2023-09-12T11:10:08,770 End of search list. 2023-09-12T11:10:08,770 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:08,771 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 2023-09-12T11:10:08,771 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:08,772 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:08,773 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:10,356 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:10,356 from include/openbabel/mol.h:43, 2023-09-12T11:10:10,357 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:10,357 from ./src/formats/unichemformat.cpp:17: 2023-09-12T11:10:10,358 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:10,358 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:10,359 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:10,360 | ^ 2023-09-12T11:10:10,360 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:10,361 37 | # define UNUSED(x) x 2023-09-12T11:10:10,361 | ^ 2023-09-12T11:10:11,123 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:11,123 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:11,124 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:11,125 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:11,125 | ^ 2023-09-12T11:10:11,126 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:11,127 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:11,128 | ^~~~~~~~ 2023-09-12T11:10:11,129 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:11,129 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:11,130 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:11,131 | ^ 2023-09-12T11:10:11,132 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:11,132 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:11,133 | ^~~~~~~~ 2023-09-12T11:10:11,147 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:11,148 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:11,148 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:11,149 | ^ 2023-09-12T11:10:11,150 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:11,151 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:11,152 | ^~~~~~~~ 2023-09-12T11:10:11,153 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:11,154 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:11,155 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:11,155 | ^ 2023-09-12T11:10:11,156 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:11,156 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:11,157 | ^~~~~~~~ 2023-09-12T11:10:11,326 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:11,326 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:11,327 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:11,328 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:11,328 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:11,329 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:11,329 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:11,330 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:11,331 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:11,332 from include/openbabel/mol.h:35: 2023-09-12T11:10:11,332 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:11,333 131 | struct binary_function 2023-09-12T11:10:11,334 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:14,040 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:10:14,041 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/ccrBWTqR.s 2023-09-12T11:10:14,045 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:14,205 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/ 2023-09-12T11:10:14,206 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/ 2023-09-12T11:10:14,206 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:10:14,207 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/formats/vaspformat.cpp -o build/temp.linux-armv7l-cpython-311/./src/formats/vaspformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2023-09-12T11:10:14,211 Using built-in specs. 2023-09-12T11:10:14,213 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:14,213 Target: arm-linux-gnueabihf 2023-09-12T11:10:14,213 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 2023-09-12T11:10:14,214 Thread model: posix 2023-09-12T11:10:14,214 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:14,215 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:14,216 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/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/' 2023-09-12T11:10:14,216 /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/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/ccQd2Igo.s 2023-09-12T11:10:14,226 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:14,226 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 2023-09-12T11:10:14,227 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:14,228 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:14,229 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:14,229 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:14,230 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:14,230 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:14,231 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:14,231 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:14,232 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:14,232 #include "..." search starts here: 2023-09-12T11:10:14,233 #include <...> search starts here: 2023-09-12T11:10:14,233 /usr/include/eigen3 2023-09-12T11:10:14,233 include 2023-09-12T11:10:14,234 /usr/include/python3.11 2023-09-12T11:10:14,234 /usr/include/c++/12 2023-09-12T11:10:14,235 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:14,235 /usr/include/c++/12/backward 2023-09-12T11:10:14,236 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:14,236 /usr/local/include 2023-09-12T11:10:14,237 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:14,237 /usr/include 2023-09-12T11:10:14,237 End of search list. 2023-09-12T11:10:14,238 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:14,238 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:14,239 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:14,240 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:14,244 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:15,821 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:15,821 from include/openbabel/mol.h:43, 2023-09-12T11:10:15,822 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:15,823 from ./src/formats/vaspformat.cpp:16: 2023-09-12T11:10:15,824 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:15,824 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:15,825 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:15,826 | ^ 2023-09-12T11:10:15,826 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:15,827 37 | # define UNUSED(x) x 2023-09-12T11:10:15,828 | ^ 2023-09-12T11:10:16,591 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:16,591 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:16,592 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:16,593 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:16,593 | ^ 2023-09-12T11:10:16,594 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:16,595 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:16,595 | ^~~~~~~~ 2023-09-12T11:10:16,597 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:16,598 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:16,599 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:16,600 | ^ 2023-09-12T11:10:16,600 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:16,601 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:16,601 | ^~~~~~~~ 2023-09-12T11:10:16,617 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:16,617 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:16,618 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:16,618 | ^ 2023-09-12T11:10:16,619 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:16,620 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:16,620 | ^~~~~~~~ 2023-09-12T11:10:16,623 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:16,624 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:16,625 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:16,625 | ^ 2023-09-12T11:10:16,626 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:16,627 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:16,628 | ^~~~~~~~ 2023-09-12T11:10:16,797 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:16,798 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:16,799 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:16,799 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:16,800 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:16,801 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:16,801 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:16,802 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:16,803 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:16,803 from include/openbabel/mol.h:35: 2023-09-12T11:10:16,804 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:16,805 131 | struct binary_function 2023-09-12T11:10:16,805 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:17,177 ./src/formats/vaspformat.cpp: In member function ‘virtual int OpenBabel::VASPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2023-09-12T11:10:17,178 ./src/formats/vaspformat.cpp:111:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2023-09-12T11:10:17,178 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:10:17,179 | ~~~~^ 2023-09-12T11:10:17,180 ./src/formats/vaspformat.cpp:111:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2023-09-12T11:10:17,180 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2023-09-12T11:10:17,181 | ~~~~~~~~~~~~~~^~~~~ 2023-09-12T11:10:17,230 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:17,231 ./src/formats/vaspformat.cpp:438:17: warning: unused variable ‘freqnum’ [-Wunused-variable] 2023-09-12T11:10:17,231 438 | int freqnum = atoi(vs[0].c_str()); 2023-09-12T11:10:17,232 | ^~~~~~~ 2023-09-12T11:10:17,237 ./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] 2023-09-12T11:10:17,237 522 | std::bind2nd(std::not_equal_to(), 0.0)); 2023-09-12T11:10:17,238 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:17,238 In file included from /usr/include/c++/12/bits/stl_function.h:1438: 2023-09-12T11:10:17,239 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:10:17,240 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:10:17,240 | ^~~~~~~ 2023-09-12T11:10:17,252 ./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] 2023-09-12T11:10:17,252 576 | std::bind2nd(std::divides(), max / 100.0)); 2023-09-12T11:10:17,253 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:17,254 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T11:10:17,254 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T11:10:17,255 | ^~~~~~~ 2023-09-12T11:10:17,271 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:17,271 ./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] 2023-09-12T11:10:17,272 657 | for(int i = 0; i < atoms_sorted.size(); i++) 2023-09-12T11:10:17,273 | ~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:17,285 ./src/formats/vaspformat.cpp:668:34: warning: suggest braces around empty body in an ‘if’ statement [-Wempty-body] 2023-09-12T11:10:17,286 668 | if(atomicNums.size() > 0); 2023-09-12T11:10:17,286 | ^ 2023-09-12T11:10:17,287 ./src/formats/vaspformat.cpp:668:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-12T11:10:17,287 668 | if(atomicNums.size() > 0); 2023-09-12T11:10:17,288 | ^~ 2023-09-12T11:10:17,289 ./src/formats/vaspformat.cpp:669:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-12T11:10:17,289 669 | atomicNums.rbegin()->second++; 2023-09-12T11:10:17,290 | ^~~~~~~~~~ 2023-09-12T11:10:21,826 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:10:21,827 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OpenBabel::matrix3x3&}; _Tp = OpenBabel::matrix3x3; _Alloc = std::allocator]’: 2023-09-12T11:10:21,828 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:21,829 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:10:21,829 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:22,070 /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]’: 2023-09-12T11:10:22,070 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:22,130 /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]’: 2023-09-12T11:10:22,131 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:24,209 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:24,210 ./src/formats/vaspformat.cpp:551:15: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:10:24,210 551 | snprintf(tag, BUFF_SIZE, "%f", pv_eV); 2023-09-12T11:10:24,211 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,212 ./src/formats/vaspformat.cpp:158:25: note: ‘pv_eV’ was declared here 2023-09-12T11:10:24,212 158 | double enthalpy_eV, pv_eV; 2023-09-12T11:10:24,213 | ^~~~~ 2023-09-12T11:10:24,214 ./src/formats/vaspformat.cpp:549:15: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:10:24,214 549 | snprintf(tag, BUFF_SIZE, "%f", enthalpy_eV); 2023-09-12T11:10:24,215 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,216 ./src/formats/vaspformat.cpp:158:12: note: ‘enthalpy_eV’ was declared here 2023-09-12T11:10:24,217 158 | double enthalpy_eV, pv_eV; 2023-09-12T11:10:24,217 | ^~~~~~~~~~~ 2023-09-12T11:10:24,218 ./src/formats/vaspformat.cpp:397:21: warning: ‘fermi’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:10:24,219 397 | dos->SetData(fermi, energies, densities, integration); 2023-09-12T11:10:24,220 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,221 ./src/formats/vaspformat.cpp:379:14: note: ‘fermi’ was declared here 2023-09-12T11:10:24,221 379 | double fermi; 2023-09-12T11:10:24,222 | ^~~~~ 2023-09-12T11:10:24,287 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,288 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, 2023-09-12T11:10:24,289 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:391:27: 2023-09-12T11:10:24,290 /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 2023-09-12T11:10:24,290 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,291 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,292 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,293 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, 2023-09-12T11:10:24,294 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:392:28: 2023-09-12T11:10:24,294 /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 2023-09-12T11:10:24,295 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,295 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,296 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,296 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, 2023-09-12T11:10:24,297 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:393:30: 2023-09-12T11:10:24,297 /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 2023-09-12T11:10:24,298 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,298 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,299 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,300 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, 2023-09-12T11:10:24,300 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:441:36: 2023-09-12T11:10:24,301 /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 2023-09-12T11:10:24,302 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,303 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,303 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,304 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, 2023-09-12T11:10:24,305 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:444:36: 2023-09-12T11:10:24,305 /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 2023-09-12T11:10:24,306 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,307 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,307 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:10:24,308 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, 2023-09-12T11:10:24,309 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:457:28: 2023-09-12T11:10:24,310 /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 2023-09-12T11:10:24,310 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,311 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,311 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:10:24,312 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, 2023-09-12T11:10:24,312 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:482:30: 2023-09-12T11:10:24,313 /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 2023-09-12T11:10:24,313 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,314 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:24,315 In file included from /usr/include/c++/12/vector:64: 2023-09-12T11:10:24,315 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::matrix3x3; _Alloc = std::allocator]’, 2023-09-12T11:10:24,316 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:503:30: 2023-09-12T11:10:24,317 /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 2023-09-12T11:10:24,317 1287 | _M_realloc_insert(end(), __x); 2023-09-12T11:10:24,318 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T11:10:24,319 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-12T11:10:24,320 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, 2023-09-12T11:10:24,320 inlined from ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/vaspformat.cpp:570:30: 2023-09-12T11:10:24,321 /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 2023-09-12T11:10:24,322 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:24,323 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:29,597 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2023-09-12T11:10:29,598 ./src/formats/vaspformat.cpp:752:26: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T11:10:29,599 752 | if (atom->HasData("move")) { 2023-09-12T11:10:29,599 | ~~~~~~~~~~~~~^~~~~~~~ 2023-09-12T11:10:29,600 ./src/formats/vaspformat.cpp:726:13: note: ‘atom’ was declared here 2023-09-12T11:10:29,601 726 | OBAtom *atom; 2023-09-12T11:10:29,601 | ^~~~ 2023-09-12T11:10:30,701 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:10:30,702 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/ccQd2Igo.s 2023-09-12T11:10:30,710 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:31,709 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/ 2023-09-12T11:10:31,709 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/ 2023-09-12T11:10:31,710 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:10:31,713 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 2023-09-12T11:10:31,718 Using built-in specs. 2023-09-12T11:10:31,719 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:31,719 Target: arm-linux-gnueabihf 2023-09-12T11:10:31,720 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 2023-09-12T11:10:31,720 Thread model: posix 2023-09-12T11:10:31,721 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:31,722 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:31,722 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:10:31,723 /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/ccE6IkkR.s 2023-09-12T11:10:31,732 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:31,732 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:31,733 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:31,733 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:31,734 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:31,735 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:31,735 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:31,736 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:31,736 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:31,737 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:31,738 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:31,738 #include "..." search starts here: 2023-09-12T11:10:31,739 #include <...> search starts here: 2023-09-12T11:10:31,739 /usr/include/eigen3 2023-09-12T11:10:31,740 include 2023-09-12T11:10:31,741 /usr/include/python3.11 2023-09-12T11:10:31,741 /usr/include/c++/12 2023-09-12T11:10:31,742 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:31,742 /usr/include/c++/12/backward 2023-09-12T11:10:31,743 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:31,744 /usr/local/include 2023-09-12T11:10:31,744 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:31,745 /usr/include 2023-09-12T11:10:31,745 End of search list. 2023-09-12T11:10:31,746 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:31,746 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:31,748 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:31,748 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:31,754 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:33,317 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:33,317 from include/openbabel/mol.h:43, 2023-09-12T11:10:33,318 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:33,319 from ./src/formats/viewmolformat.cpp:17: 2023-09-12T11:10:33,320 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:33,320 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:33,321 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:33,322 | ^ 2023-09-12T11:10:33,322 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:33,323 37 | # define UNUSED(x) x 2023-09-12T11:10:33,323 | ^ 2023-09-12T11:10:34,087 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:34,087 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:34,088 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:34,089 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:34,089 | ^ 2023-09-12T11:10:34,090 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:34,090 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:34,091 | ^~~~~~~~ 2023-09-12T11:10:34,093 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:34,094 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:34,094 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:34,095 | ^ 2023-09-12T11:10:34,096 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:34,097 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:34,098 | ^~~~~~~~ 2023-09-12T11:10:34,113 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:34,114 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:34,115 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:34,116 | ^ 2023-09-12T11:10:34,116 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:34,117 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:34,118 | ^~~~~~~~ 2023-09-12T11:10:34,121 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:34,121 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:34,122 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:34,123 | ^ 2023-09-12T11:10:34,124 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:34,124 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:34,125 | ^~~~~~~~ 2023-09-12T11:10:34,295 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:34,295 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:34,296 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:34,296 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:34,297 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:34,297 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:34,298 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:34,299 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:34,299 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:34,300 from include/openbabel/mol.h:35: 2023-09-12T11:10:34,300 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:34,301 131 | struct binary_function 2023-09-12T11:10:34,301 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:37,029 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/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/' 2023-09-12T11:10:37,030 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/ccE6IkkR.s 2023-09-12T11:10:37,035 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:37,190 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/ 2023-09-12T11:10:37,190 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/ 2023-09-12T11:10:37,191 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:10:37,192 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 2023-09-12T11:10:37,196 Using built-in specs. 2023-09-12T11:10:37,197 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:37,197 Target: arm-linux-gnueabihf 2023-09-12T11:10:37,198 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 2023-09-12T11:10:37,199 Thread model: posix 2023-09-12T11:10:37,199 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:37,200 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:37,200 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:10:37,201 /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/cceqXlwB.s 2023-09-12T11:10:37,209 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:37,210 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:37,211 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:37,212 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:37,212 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:37,213 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:37,213 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:37,214 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:37,214 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:37,215 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:37,215 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:37,216 #include "..." search starts here: 2023-09-12T11:10:37,217 #include <...> search starts here: 2023-09-12T11:10:37,217 /usr/include/eigen3 2023-09-12T11:10:37,218 include 2023-09-12T11:10:37,218 /usr/include/python3.11 2023-09-12T11:10:37,219 /usr/include/c++/12 2023-09-12T11:10:37,220 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:37,220 /usr/include/c++/12/backward 2023-09-12T11:10:37,221 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:37,222 /usr/local/include 2023-09-12T11:10:37,223 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:37,223 /usr/include 2023-09-12T11:10:37,223 End of search list. 2023-09-12T11:10:37,224 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:37,224 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:37,225 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:37,225 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:37,229 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:38,829 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:38,830 from include/openbabel/mol.h:43, 2023-09-12T11:10:38,831 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:38,831 from ./src/formats/xedformat.cpp:17: 2023-09-12T11:10:38,832 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:38,832 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:38,833 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:38,833 | ^ 2023-09-12T11:10:38,834 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:38,834 37 | # define UNUSED(x) x 2023-09-12T11:10:38,835 | ^ 2023-09-12T11:10:39,602 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:39,602 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:39,603 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:39,604 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:39,605 | ^ 2023-09-12T11:10:39,605 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:39,606 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:39,607 | ^~~~~~~~ 2023-09-12T11:10:39,608 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:39,609 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:39,610 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:39,610 | ^ 2023-09-12T11:10:39,611 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:39,612 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:39,613 | ^~~~~~~~ 2023-09-12T11:10:39,629 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:39,629 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:39,630 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:39,631 | ^ 2023-09-12T11:10:39,632 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:39,633 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:39,633 | ^~~~~~~~ 2023-09-12T11:10:39,636 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:39,637 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:39,637 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:39,638 | ^ 2023-09-12T11:10:39,638 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:39,639 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:39,640 | ^~~~~~~~ 2023-09-12T11:10:39,810 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:39,810 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:39,811 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:39,812 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:39,812 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:39,813 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:39,814 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:39,815 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:39,815 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:39,816 from include/openbabel/mol.h:35: 2023-09-12T11:10:39,817 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:39,818 131 | struct binary_function 2023-09-12T11:10:39,818 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:42,343 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/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/' 2023-09-12T11:10:42,344 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/xedformat.o /tmp/cceqXlwB.s 2023-09-12T11:10:42,348 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:42,494 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/ 2023-09-12T11:10:42,494 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/ 2023-09-12T11:10:42,495 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:10:42,496 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 2023-09-12T11:10:42,500 Using built-in specs. 2023-09-12T11:10:42,500 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:42,501 Target: arm-linux-gnueabihf 2023-09-12T11:10:42,501 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 2023-09-12T11:10:42,502 Thread model: posix 2023-09-12T11:10:42,502 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:42,503 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:42,503 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2023-09-12T11:10:42,504 /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/ccj1Z10q.s 2023-09-12T11:10:42,513 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:42,514 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:42,515 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:42,515 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:42,516 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:42,517 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:42,517 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:42,518 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:42,518 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:42,518 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:42,519 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:42,519 #include "..." search starts here: 2023-09-12T11:10:42,520 #include <...> search starts here: 2023-09-12T11:10:42,520 /usr/include/eigen3 2023-09-12T11:10:42,521 include 2023-09-12T11:10:42,521 /usr/include/python3.11 2023-09-12T11:10:42,522 /usr/include/c++/12 2023-09-12T11:10:42,522 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:42,522 /usr/include/c++/12/backward 2023-09-12T11:10:42,523 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:42,523 /usr/local/include 2023-09-12T11:10:42,524 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:42,524 /usr/include 2023-09-12T11:10:42,525 End of search list. 2023-09-12T11:10:42,525 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:42,526 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:42,527 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:42,527 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:42,534 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:44,093 In file included from include/openbabel/atom.h:33, 2023-09-12T11:10:44,093 from include/openbabel/mol.h:43, 2023-09-12T11:10:44,094 from include/openbabel/obmolecformat.h:26, 2023-09-12T11:10:44,095 from ./src/formats/xsfformat.cpp:16: 2023-09-12T11:10:44,096 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2023-09-12T11:10:44,096 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2023-09-12T11:10:44,097 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2023-09-12T11:10:44,098 | ^ 2023-09-12T11:10:44,099 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2023-09-12T11:10:44,099 37 | # define UNUSED(x) x 2023-09-12T11:10:44,100 | ^ 2023-09-12T11:10:44,863 In file included from include/openbabel/mol.h:52: 2023-09-12T11:10:44,864 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:44,864 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:44,865 862 | {return new OBVibrationData(*this);} 2023-09-12T11:10:44,866 | ^ 2023-09-12T11:10:44,866 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2023-09-12T11:10:44,867 864 | OBVibrationData & operator=(const OBVibrationData &); 2023-09-12T11:10:44,868 | ^~~~~~~~ 2023-09-12T11:10:44,869 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:44,870 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:44,871 907 | {return new OBDOSData(*this);} 2023-09-12T11:10:44,871 | ^ 2023-09-12T11:10:44,872 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2023-09-12T11:10:44,872 909 | OBDOSData & operator=(const OBDOSData &); 2023-09-12T11:10:44,873 | ^~~~~~~~ 2023-09-12T11:10:44,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:44,890 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:44,890 954 | {return new OBOrbitalData(*this);} 2023-09-12T11:10:44,891 | ^ 2023-09-12T11:10:44,891 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2023-09-12T11:10:44,892 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2023-09-12T11:10:44,892 | ^~~~~~~~ 2023-09-12T11:10:44,896 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2023-09-12T11:10:44,897 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2023-09-12T11:10:44,898 1014 | {return new OBElectronicTransitionData(*this);} 2023-09-12T11:10:44,899 | ^ 2023-09-12T11:10:44,899 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2023-09-12T11:10:44,900 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2023-09-12T11:10:44,901 | ^~~~~~~~ 2023-09-12T11:10:45,070 In file included from include/openbabel/format.h:22, 2023-09-12T11:10:45,071 from include/openbabel/obconversion.h:37, 2023-09-12T11:10:45,071 from include/openbabel/obmolecformat.h:31: 2023-09-12T11:10:45,072 include/openbabel/plugin.h: At global scope: 2023-09-12T11:10:45,073 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2023-09-12T11:10:45,073 40 | struct OBERROR CharPtrLess : public std::binary_function 2023-09-12T11:10:45,074 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:45,075 In file included from /usr/include/c++/12/bits/refwrap.h:39, 2023-09-12T11:10:45,075 from /usr/include/c++/12/vector:66, 2023-09-12T11:10:45,076 from include/openbabel/mol.h:35: 2023-09-12T11:10:45,077 /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 2023-09-12T11:10:45,077 131 | struct binary_function 2023-09-12T11:10:45,078 | ^~~~~~~~~~~~~~~ 2023-09-12T11:10:47,551 In file included from /usr/include/c++/12/vector:70: 2023-09-12T11:10:47,552 /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]’: 2023-09-12T11:10:47,553 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T11:10:47,554 439 | vector<_Tp, _Alloc>:: 2023-09-12T11:10:47,554 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:47,759 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:10:47,760 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, 2023-09-12T11:10:47,760 inlined from ‘virtual bool OpenBabel::XSFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/xsfformat.cpp:104:36: 2023-09-12T11:10:47,761 /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 2023-09-12T11:10:47,762 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:47,762 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:47,763 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {OpenBabel::vector3}; _Tp = OpenBabel::vector3; _Alloc = std::allocator]’, 2023-09-12T11:10:47,763 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, 2023-09-12T11:10:47,764 inlined from ‘virtual bool OpenBabel::XSFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/xsfformat.cpp:145:36: 2023-09-12T11:10:47,765 /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 2023-09-12T11:10:47,765 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T11:10:47,766 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T11:10:48,193 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/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/' 2023-09-12T11:10:48,194 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/xsfformat.o /tmp/ccj1Z10q.s 2023-09-12T11:10:48,198 GNU assembler version 2.40 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.40 2023-09-12T11:10:48,390 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/ 2023-09-12T11:10:48,391 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/ 2023-09-12T11:10:48,391 COLLECT_GCC_OPTIONS='-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-g' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-g' '-fwrapv' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2023-09-12T11:10:48,393 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 2023-09-12T11:10:48,397 Using built-in specs. 2023-09-12T11:10:48,397 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-12T11:10:48,398 Target: arm-linux-gnueabihf 2023-09-12T11:10:48,398 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 2023-09-12T11:10:48,399 Thread model: posix 2023-09-12T11:10:48,400 Supported LTO compression algorithms: zlib zstd 2023-09-12T11:10:48,400 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-12T11:10:48,401 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/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/' 2023-09-12T11:10:48,401 /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/cclaNKgg.s 2023-09-12T11:10:48,410 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:48,411 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 2023-09-12T11:10:48,412 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:48,413 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:48,413 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/12" 2023-09-12T11:10:48,414 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2023-09-12T11:10:48,415 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/include-fixed" 2023-09-12T11:10:48,415 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/include" 2023-09-12T11:10:48,415 ignoring duplicate directory "/usr/include/" 2023-09-12T11:10:48,416 as it is a non-system directory that duplicates a system directory 2023-09-12T11:10:48,416 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2023-09-12T11:10:48,417 #include "..." search starts here: 2023-09-12T11:10:48,417 #include <...> search starts here: 2023-09-12T11:10:48,418 /usr/include/eigen3 2023-09-12T11:10:48,418 include 2023-09-12T11:10:48,419 /usr/include/python3.11 2023-09-12T11:10:48,419 /usr/include/c++/12 2023-09-12T11:10:48,419 /usr/include/arm-linux-gnueabihf/c++/12 2023-09-12T11:10:48,420 /usr/include/c++/12/backward 2023-09-12T11:10:48,420 /usr/lib/gcc/arm-linux-gnueabihf/12/include 2023-09-12T11:10:48,421 /usr/local/include 2023-09-12T11:10:48,421 /usr/include/arm-linux-gnueabihf 2023-09-12T11:10:48,422 /usr/include 2023-09-12T11:10:48,422 End of search list. 2023-09-12T11:10:48,423 GNU C++14 (Raspbian 12.2.0-14+rpi1) version 12.2.0 (arm-linux-gnueabihf) 2023-09-12T11:10:48,423 compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP 2023-09-12T11:10:48,424 warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 2023-09-12T11:10:48,425 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2023-09-12T11:10:48,430 Compiler executable checksum: 35b9a090b216240322859958bccd87d7 2023-09-12T11:10:48,772 ./src/formats/xtcformat.cpp:23:10: fatal error: rpc/types.h: No such file or directory 2023-09-12T11:10:48,773 23 | #include 2023-09-12T11:10:48,773 | ^~~~~~~~~~~~~ 2023-09-12T11:10:48,774 compilation terminated. 2023-09-12T11:10:48,779 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-12T11:10:48,932 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-12T11:10:48,945 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-12T11:10:48,945 exec(compile('"'"''"'"''"'"' 2023-09-12T11:10:48,945 # This is -- a caller that pip uses to run setup.py 2023-09-12T11:10:48,945 # 2023-09-12T11:10:48,945 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-12T11:10:48,945 # import from `distutils.core` to work with newer packaging standards. 2023-09-12T11:10:48,945 # - It provides a clear error message when setuptools is not installed. 2023-09-12T11:10:48,945 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-12T11:10:48,945 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-12T11:10:48,945 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-12T11:10:48,945 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-12T11:10:48,945 import os, sys, tokenize 2023-09-12T11:10:48,945 2023-09-12T11:10:48,945 try: 2023-09-12T11:10:48,945 import setuptools 2023-09-12T11:10:48,945 except ImportError as error: 2023-09-12T11:10:48,945 print( 2023-09-12T11:10:48,945 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-12T11:10:48,945 "the build environment.", 2023-09-12T11:10:48,945 file=sys.stderr, 2023-09-12T11:10:48,945 ) 2023-09-12T11:10:48,945 sys.exit(1) 2023-09-12T11:10:48,945 2023-09-12T11:10:48,945 __file__ = %r 2023-09-12T11:10:48,945 sys.argv[0] = __file__ 2023-09-12T11:10:48,945 2023-09-12T11:10:48,945 if os.path.exists(__file__): 2023-09-12T11:10:48,945 filename = __file__ 2023-09-12T11:10:48,945 with tokenize.open(__file__) as f: 2023-09-12T11:10:48,945 setup_py_code = f.read() 2023-09-12T11:10:48,945 else: 2023-09-12T11:10:48,945 filename = "" 2023-09-12T11:10:48,945 setup_py_code = "from setuptools import setup; setup()" 2023-09-12T11:10:48,945 2023-09-12T11:10:48,945 exec(compile(setup_py_code, filename, "exec")) 2023-09-12T11:10:48,945 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-v347_ll_/maagbel_ac2148b3a028460ebbf8680210360358/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-gnlrmcc0[/] 2023-09-12T11:10:48,946 [bold magenta]cwd[/]: /tmp/pip-wheel-v347_ll_/maagbel_ac2148b3a028460ebbf8680210360358/ 2023-09-12T11:10:48,947 Building wheel for maagbel (setup.py): finished with status 'error' 2023-09-12T11:10:48,948 ERROR: Failed building wheel for maagbel 2023-09-12T11:10:48,950 Running setup.py clean for maagbel 2023-09-12T11:10:48,951 Running command python setup.py clean 2023-09-12T11:10:49,501 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'mail' 2023-09-12T11:10:49,501 warnings.warn(msg) 2023-09-12T11:10:50,037 running clean 2023-09-12T11:10:50,060 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-12T11:10:50,142 'build/lib.linux-armv7l-cpython-311' does not exist -- can't clean it 2023-09-12T11:10:50,143 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-12T11:10:50,143 'build/scripts-3.11' does not exist -- can't clean it 2023-09-12T11:10:50,144 removing 'build' 2023-09-12T11:10:50,250 Failed to build maagbel 2023-09-12T11:10:50,252 ERROR: Failed to build one or more wheels 2023-09-12T11:10:50,253 Exception information: 2023-09-12T11:10:50,253 Traceback (most recent call last): 2023-09-12T11:10:50,253 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-12T11:10:50,253 status = run_func(*args) 2023-09-12T11:10:50,253 ^^^^^^^^^^^^^^^ 2023-09-12T11:10:50,253 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-12T11:10:50,253 return func(self, options, args) 2023-09-12T11:10:50,253 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T11:10:50,253 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-12T11:10:50,253 raise CommandError("Failed to build one or more wheels") 2023-09-12T11:10:50,253 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-12T11:10:50,257 Removed build tracker: '/tmp/pip-build-tracker-21zxo5rz'