2025-09-09T00:31:57,730 Created temporary directory: /tmp/pip-build-tracker-b88b9ob_ 2025-09-09T00:31:57,731 Initialized build tracking at /tmp/pip-build-tracker-b88b9ob_ 2025-09-09T00:31:57,731 Created build tracker: /tmp/pip-build-tracker-b88b9ob_ 2025-09-09T00:31:57,731 Entered build tracker: /tmp/pip-build-tracker-b88b9ob_ 2025-09-09T00:31:57,731 Created temporary directory: /tmp/pip-wheel-38rab5zi 2025-09-09T00:31:57,734 Created temporary directory: /tmp/pip-ephem-wheel-cache-0tmsh8gn 2025-09-09T00:31:57,791 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-09T00:31:57,793 2 location(s) to search for versions of maagbel: 2025-09-09T00:31:57,793 * https://pypi.org/simple/maagbel/ 2025-09-09T00:31:57,793 * https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:31:57,794 Fetching project page and analyzing links: https://pypi.org/simple/maagbel/ 2025-09-09T00:31:57,794 Getting page https://pypi.org/simple/maagbel/ 2025-09-09T00:31:57,795 Found index url https://pypi.org/simple/ 2025-09-09T00:31:57,873 Fetched page https://pypi.org/simple/maagbel/ as application/vnd.pypi.simple.v1+json 2025-09-09T00:31:57,874 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 2025-09-09T00:31:57,874 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 2025-09-09T00:31:57,875 Fetching project page and analyzing links: https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:31:57,875 Getting page https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:31:57,876 Found index url https://www.piwheels.org/simple/ 2025-09-09T00:31:57,972 Fetched page https://www.piwheels.org/simple/maagbel/ as text/html 2025-09-09T00:31:57,973 Skipping link: not a file: https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:31:57,973 Skipping link: not a file: https://pypi.org/simple/maagbel/ 2025-09-09T00:31:57,996 Given no hashes to check 1 links for project 'maagbel': discarding no candidates 2025-09-09T00:31:57,997 Collecting maagbel==0.1.2 2025-09-09T00:31:57,999 Created temporary directory: /tmp/pip-unpack-93s72xqv 2025-09-09T00:31:58,141 Downloading maagbel-0.1.2.tar.gz (1.8 MB) 2025-09-09T00:31:58,769 Added maagbel==0.1.2 from https://files.pythonhosted.org/packages/56/df/95416ae78c46c743df0739d430805645965f57b4cee30083ac8ff9c1ece7/maagbel-0.1.2.tar.gz to build tracker '/tmp/pip-build-tracker-b88b9ob_' 2025-09-09T00:31:58,770 Running setup.py (path:/tmp/pip-wheel-38rab5zi/maagbel_5dfce457d0e44020bbc659fc751f0b87/setup.py) egg_info for package maagbel 2025-09-09T00:31:58,770 Created temporary directory: /tmp/pip-pip-egg-info-164rz375 2025-09-09T00:31:58,770 Preparing metadata (setup.py): started 2025-09-09T00:31:58,771 Running command python setup.py egg_info 2025-09-09T00:31:59,500 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'mail' 2025-09-09T00:31:59,500 warnings.warn(msg) 2025-09-09T00:31:59,887 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T00:31:59,887 !! 2025-09-09T00:31:59,887 ******************************************************************************** 2025-09-09T00:31:59,887 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T00:31:59,888 License :: OSI Approved :: GNU General Public License v2 (GPLv2) 2025-09-09T00:31:59,888 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T00:31:59,888 ******************************************************************************** 2025-09-09T00:31:59,888 !! 2025-09-09T00:31:59,888 self._finalize_license_expression() 2025-09-09T00:31:59,961 running egg_info 2025-09-09T00:32:00,038 creating /tmp/pip-pip-egg-info-164rz375/maagbel.egg-info 2025-09-09T00:32:00,038 writing /tmp/pip-pip-egg-info-164rz375/maagbel.egg-info/PKG-INFO 2025-09-09T00:32:00,039 writing dependency_links to /tmp/pip-pip-egg-info-164rz375/maagbel.egg-info/dependency_links.txt 2025-09-09T00:32:00,040 writing top-level names to /tmp/pip-pip-egg-info-164rz375/maagbel.egg-info/top_level.txt 2025-09-09T00:32:00,041 writing manifest file '/tmp/pip-pip-egg-info-164rz375/maagbel.egg-info/SOURCES.txt' 2025-09-09T00:32:00,296 reading manifest file '/tmp/pip-pip-egg-info-164rz375/maagbel.egg-info/SOURCES.txt' 2025-09-09T00:32:00,297 reading manifest template 'MANIFEST.in' 2025-09-09T00:32:00,315 writing manifest file '/tmp/pip-pip-egg-info-164rz375/maagbel.egg-info/SOURCES.txt' 2025-09-09T00:32:00,429 Preparing metadata (setup.py): finished with status 'done' 2025-09-09T00:32:00,434 Source in /tmp/pip-wheel-38rab5zi/maagbel_5dfce457d0e44020bbc659fc751f0b87 has version 0.1.2, which satisfies requirement maagbel==0.1.2 from https://files.pythonhosted.org/packages/56/df/95416ae78c46c743df0739d430805645965f57b4cee30083ac8ff9c1ece7/maagbel-0.1.2.tar.gz 2025-09-09T00:32:00,434 Removed maagbel==0.1.2 from https://files.pythonhosted.org/packages/56/df/95416ae78c46c743df0739d430805645965f57b4cee30083ac8ff9c1ece7/maagbel-0.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-b88b9ob_' 2025-09-09T00:32:00,437 Created temporary directory: /tmp/pip-unpack-1ogqf4z0 2025-09-09T00:32:00,437 Created temporary directory: /tmp/pip-unpack-q8mipm8k 2025-09-09T00:32:00,438 Building wheels for collected packages: maagbel 2025-09-09T00:32:00,439 Created temporary directory: /tmp/pip-wheel-vo9bbe93 2025-09-09T00:32:00,439 DEPRECATION: Building 'maagbel' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'maagbel'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-09T00:32:00,440 Building wheel for maagbel (setup.py): started 2025-09-09T00:32:00,441 Destination directory: /tmp/pip-wheel-vo9bbe93 2025-09-09T00:32:00,441 Running command python setup.py bdist_wheel 2025-09-09T00:32:01,212 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'mail' 2025-09-09T00:32:01,212 warnings.warn(msg) 2025-09-09T00:32:01,593 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T00:32:01,593 !! 2025-09-09T00:32:01,593 ******************************************************************************** 2025-09-09T00:32:01,594 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T00:32:01,594 License :: OSI Approved :: GNU General Public License v2 (GPLv2) 2025-09-09T00:32:01,594 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T00:32:01,594 ******************************************************************************** 2025-09-09T00:32:01,594 !! 2025-09-09T00:32:01,594 self._finalize_license_expression() 2025-09-09T00:32:01,595 running bdist_wheel 2025-09-09T00:32:01,887 running build 2025-09-09T00:32:01,887 running build_ext 2025-09-09T00:32:02,251 building 'maagbel._cpp' extension 2025-09-09T00:32:02,252 swigging maagbel/cpp.i to maagbel/cpp_wrap.cpp 2025-09-09T00:32:02,252 swig -python -c++ -Iinclude -o maagbel/cpp_wrap.cpp maagbel/cpp.i 2025-09-09T00:32:04,957 include/openbabel/obconversion.h:369: Warning 325: Nested struct not currently supported (StreamState ignored) 2025-09-09T00:32:06,022 include/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored) 2025-09-09T00:32:06,274 include/openbabel/spectrophore.h:571: Warning 312: Nested struct not currently supported (ignored). 2025-09-09T00:32:06,276 include/openbabel/spectrophore.h:578: Warning 312: Nested struct not currently supported (ignored). 2025-09-09T00:32:28,865 creating build/temp.linux-armv7l-cpython-313/src 2025-09-09T00:32:28,867 creating build/temp.linux-armv7l-cpython-313/src/charges 2025-09-09T00:32:28,868 creating build/temp.linux-armv7l-cpython-313/src/depict 2025-09-09T00:32:28,869 creating build/temp.linux-armv7l-cpython-313/src/descriptors 2025-09-09T00:32:28,870 creating build/temp.linux-armv7l-cpython-313/src/fingerprints 2025-09-09T00:32:28,870 creating build/temp.linux-armv7l-cpython-313/src/forcefields 2025-09-09T00:32:28,871 creating build/temp.linux-armv7l-cpython-313/src/formats 2025-09-09T00:32:28,880 creating build/temp.linux-armv7l-cpython-313/src/math 2025-09-09T00:32:28,882 creating build/temp.linux-armv7l-cpython-313/src/ops 2025-09-09T00:32:28,885 creating build/temp.linux-armv7l-cpython-313/src/stereo 2025-09-09T00:32:28,886 creating build/temp.linux-armv7l-cpython-313/maagbel 2025-09-09T00:32:28,886 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/aggregate.cpp -o build/temp.linux-armv7l-cpython-313/src/aggregate.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:32:28,892 Using built-in specs. 2025-09-09T00:32:28,892 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:28,893 Target: arm-linux-gnueabihf 2025-09-09T00:32:28,893 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:32:28,893 Thread model: posix 2025-09-09T00:32:28,893 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:28,893 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:28,893 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/aggregate.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:28,893 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/aggregate.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase aggregate.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccK2rtKl.s 2025-09-09T00:32:28,905 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:28,905 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:32:28,906 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:28,906 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:28,907 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:28,907 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:28,907 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:28,907 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:28,908 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:28,908 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:28,908 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:28,908 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:28,908 #include "..." search starts here: 2025-09-09T00:32:28,908 #include <...> search starts here: 2025-09-09T00:32:28,909 /usr/include/eigen3 2025-09-09T00:32:28,909 include 2025-09-09T00:32:28,909 /usr/include/python3.13 2025-09-09T00:32:28,909 /usr/include/c++/14 2025-09-09T00:32:28,909 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:28,909 /usr/include/c++/14/backward 2025-09-09T00:32:28,909 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:28,910 /usr/local/include 2025-09-09T00:32:28,910 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:28,910 /usr/include 2025-09-09T00:32:28,910 End of search list. 2025-09-09T00:32:28,927 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:30,473 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:30,474 from include/openbabel/mol.h:43, 2025-09-09T00:32:30,474 from ./src/aggregate.cpp:20: 2025-09-09T00:32:30,474 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:30,474 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:30,474 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:30,474 | ^ 2025-09-09T00:32:30,474 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:30,474 37 | # define UNUSED(x) x 2025-09-09T00:32:30,474 | ^ 2025-09-09T00:32:31,087 In file included from include/openbabel/mol.h:52: 2025-09-09T00:32:31,088 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:31,088 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:31,088 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:31,088 | ^ 2025-09-09T00:32:31,088 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:31,088 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:31,088 | ^~~~~~~~ 2025-09-09T00:32:31,091 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:31,091 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:31,092 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:31,092 | ^ 2025-09-09T00:32:31,092 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:31,092 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:31,092 | ^~~~~~~~ 2025-09-09T00:32:31,106 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:31,106 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:31,106 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:31,106 | ^ 2025-09-09T00:32:31,106 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:31,106 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:31,106 | ^~~~~~~~ 2025-09-09T00:32:31,111 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:31,111 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:31,111 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:31,111 | ^ 2025-09-09T00:32:31,111 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:31,111 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:31,111 | ^~~~~~~~ 2025-09-09T00:32:31,288 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:32:31,288 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:32:31,289 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:32:31,289 | ^ 2025-09-09T00:32:31,289 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:31,289 37 | # define UNUSED(x) x 2025-09-09T00:32:31,289 | ^ 2025-09-09T00:32:31,289 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:32:31,289 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:32:31,289 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:32:31,289 | ^ 2025-09-09T00:32:31,290 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:31,290 37 | # define UNUSED(x) x 2025-09-09T00:32:31,290 | ^ 2025-09-09T00:32:31,555 ./src/aggregate.cpp: In member function ‘float OpenBabel::OBAggregate::MinVDWDist(bool, double)’: 2025-09-09T00:32:31,556 ./src/aggregate.cpp:151:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:32:31,556 151 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2025-09-09T00:32:31,556 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:31,556 ./src/aggregate.cpp:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:32:31,556 156 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2025-09-09T00:32:31,556 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:31,564 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’: 2025-09-09T00:32:31,564 ./src/aggregate.cpp:245:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:32:31,564 245 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2025-09-09T00:32:31,564 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:31,580 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::FindAllConnections(bool)’: 2025-09-09T00:32:31,580 ./src/aggregate.cpp:316:20: warning: unused variable ‘a’ [-Wunused-variable] 2025-09-09T00:32:31,580 316 | OBAtom *atom, *a; 2025-09-09T00:32:31,580 | ^ 2025-09-09T00:32:31,599 ./src/aggregate.cpp: In member function ‘std::string OpenBabel::OBAggregate::GetConnections()’: 2025-09-09T00:32:31,599 ./src/aggregate.cpp:558:13: warning: unused variable ‘id’ [-Wunused-variable] 2025-09-09T00:32:31,599 558 | int id = -1; 2025-09-09T00:32:31,599 | ^~ 2025-09-09T00:32:31,600 ./src/aggregate.cpp:559:13: warning: unused variable ‘elements’ [-Wunused-variable] 2025-09-09T00:32:31,600 559 | int elements = 0; 2025-09-09T00:32:31,600 | ^~~~~~~~ 2025-09-09T00:32:31,603 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::PrintConnections()’: 2025-09-09T00:32:31,603 ./src/aggregate.cpp:584:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:32:31,603 584 | if ( atom->GetIdx() != id+1 ){ 2025-09-09T00:32:31,603 | ~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:32:31,625 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::AddToTag(int, int)’: 2025-09-09T00:32:31,625 ./src/aggregate.cpp:772:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:32:31,626 772 | if (tag >= _molTags.size() || tag<0){ 2025-09-09T00:32:31,626 | ~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:39,244 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/aggregate.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:39,244 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/aggregate.o /tmp/ccK2rtKl.s 2025-09-09T00:32:39,249 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:39,874 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:32:39,874 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:32:39,874 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/aggregate.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/aggregate.' 2025-09-09T00:32:39,876 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/alias.cpp -o build/temp.linux-armv7l-cpython-313/src/alias.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:32:39,881 Using built-in specs. 2025-09-09T00:32:39,882 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:39,882 Target: arm-linux-gnueabihf 2025-09-09T00:32:39,882 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:32:39,882 Thread model: posix 2025-09-09T00:32:39,882 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:39,882 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:39,882 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/alias.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:39,882 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/alias.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase alias.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccNkLpX9.s 2025-09-09T00:32:39,893 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:39,893 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:32:39,893 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:39,893 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:39,894 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:39,894 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:39,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:39,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:39,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:39,894 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:39,894 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:39,895 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:39,895 #include "..." search starts here: 2025-09-09T00:32:39,895 #include <...> search starts here: 2025-09-09T00:32:39,895 /usr/include/eigen3 2025-09-09T00:32:39,895 include 2025-09-09T00:32:39,895 /usr/include/python3.13 2025-09-09T00:32:39,895 /usr/include/c++/14 2025-09-09T00:32:39,896 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:39,896 /usr/include/c++/14/backward 2025-09-09T00:32:39,896 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:39,896 /usr/local/include 2025-09-09T00:32:39,896 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:39,896 /usr/include 2025-09-09T00:32:39,896 End of search list. 2025-09-09T00:32:39,913 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:41,569 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:41,570 from include/openbabel/mol.h:43, 2025-09-09T00:32:41,570 from include/openbabel/alias.h:20, 2025-09-09T00:32:41,570 from ./src/alias.cpp:17: 2025-09-09T00:32:41,570 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:41,570 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:41,570 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:41,570 | ^ 2025-09-09T00:32:41,570 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:41,571 37 | # define UNUSED(x) x 2025-09-09T00:32:41,571 | ^ 2025-09-09T00:32:42,182 In file included from include/openbabel/mol.h:52: 2025-09-09T00:32:42,182 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:42,183 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:42,183 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:42,183 | ^ 2025-09-09T00:32:42,183 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:42,183 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:42,183 | ^~~~~~~~ 2025-09-09T00:32:42,186 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:42,186 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:42,186 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:42,187 | ^ 2025-09-09T00:32:42,187 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:42,187 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:42,187 | ^~~~~~~~ 2025-09-09T00:32:42,201 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:42,201 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:42,201 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:42,201 | ^ 2025-09-09T00:32:42,201 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:42,201 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:42,202 | ^~~~~~~~ 2025-09-09T00:32:42,206 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:42,206 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:42,206 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:42,206 | ^ 2025-09-09T00:32:42,206 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:42,206 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:42,206 | ^~~~~~~~ 2025-09-09T00:32:42,375 In file included from include/openbabel/format.h:22, 2025-09-09T00:32:42,375 from include/openbabel/obconversion.h:37, 2025-09-09T00:32:42,375 from ./src/alias.cpp:18: 2025-09-09T00:32:42,375 include/openbabel/plugin.h: At global scope: 2025-09-09T00:32:42,375 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:32:42,375 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:32:42,375 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:42,375 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:32:42,376 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:32:42,376 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:32:42,376 from /usr/include/c++/14/ios:44, 2025-09-09T00:32:42,376 from /usr/include/c++/14/istream:40, 2025-09-09T00:32:42,376 from /usr/include/c++/14/sstream:40, 2025-09-09T00:32:42,376 from ./src/alias.cpp:15: 2025-09-09T00:32:42,376 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:32:42,376 131 | struct binary_function 2025-09-09T00:32:42,376 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:46,927 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/alias.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:46,927 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/alias.o /tmp/ccNkLpX9.s 2025-09-09T00:32:46,933 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:47,313 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:32:47,313 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:32:47,313 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/alias.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/alias.' 2025-09-09T00:32:47,315 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/atom.cpp -o build/temp.linux-armv7l-cpython-313/src/atom.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:32:47,319 Using built-in specs. 2025-09-09T00:32:47,320 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:47,320 Target: arm-linux-gnueabihf 2025-09-09T00:32:47,320 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:32:47,320 Thread model: posix 2025-09-09T00:32:47,320 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:47,320 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:47,320 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/atom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:47,320 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/atom.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase atom.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccPFHS0L.s 2025-09-09T00:32:47,330 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:47,330 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:32:47,330 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:47,330 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:47,330 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:47,330 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:47,330 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:47,331 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:47,331 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:47,331 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:47,331 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:47,331 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:47,331 #include "..." search starts here: 2025-09-09T00:32:47,331 #include <...> search starts here: 2025-09-09T00:32:47,331 /usr/include/eigen3 2025-09-09T00:32:47,331 include 2025-09-09T00:32:47,331 /usr/include/python3.13 2025-09-09T00:32:47,332 /usr/include/c++/14 2025-09-09T00:32:47,332 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:47,332 /usr/include/c++/14/backward 2025-09-09T00:32:47,332 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:47,332 /usr/local/include 2025-09-09T00:32:47,332 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:47,332 /usr/include 2025-09-09T00:32:47,332 End of search list. 2025-09-09T00:32:47,345 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:48,756 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:48,756 from ./src/atom.cpp:22: 2025-09-09T00:32:48,757 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:48,757 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:48,757 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:48,757 | ^ 2025-09-09T00:32:48,757 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:48,757 37 | # define UNUSED(x) x 2025-09-09T00:32:48,757 | ^ 2025-09-09T00:32:49,432 In file included from include/openbabel/mol.h:52, 2025-09-09T00:32:49,432 from include/openbabel/isomorphism.h:27, 2025-09-09T00:32:49,433 from include/openbabel/stereo/stereo.h:28, 2025-09-09T00:32:49,433 from ./src/atom.cpp:23: 2025-09-09T00:32:49,433 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:49,433 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:49,433 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:49,433 | ^ 2025-09-09T00:32:49,433 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:49,433 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:49,433 | ^~~~~~~~ 2025-09-09T00:32:49,436 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:49,436 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:49,436 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:49,436 | ^ 2025-09-09T00:32:49,437 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:49,437 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:49,437 | ^~~~~~~~ 2025-09-09T00:32:49,451 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:49,451 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:49,451 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:49,451 | ^ 2025-09-09T00:32:49,451 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:49,451 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:49,451 | ^~~~~~~~ 2025-09-09T00:32:49,455 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:49,456 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:49,456 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:49,456 | ^ 2025-09-09T00:32:49,456 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:49,456 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:49,456 | ^~~~~~~~ 2025-09-09T00:32:49,744 ./src/atom.cpp: In member function ‘int OpenBabel::OBAtom::HighestBondOrder()’: 2025-09-09T00:32:49,745 ./src/atom.cpp:302:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:32:49,745 302 | if(bond->GetBO() > highest) 2025-09-09T00:32:49,745 | ~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:32:55,653 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/atom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:55,653 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/atom.o /tmp/ccPFHS0L.s 2025-09-09T00:32:55,658 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:56,153 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:32:56,153 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:32:56,153 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/atom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/atom.' 2025-09-09T00:32:56,155 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/base.cpp -o build/temp.linux-armv7l-cpython-313/src/base.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:32:56,159 Using built-in specs. 2025-09-09T00:32:56,160 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:56,161 Target: arm-linux-gnueabihf 2025-09-09T00:32:56,161 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:32:56,161 Thread model: posix 2025-09-09T00:32:56,161 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:56,161 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:56,162 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/base.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:56,164 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/base.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase base.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc92cpEW.s 2025-09-09T00:32:56,175 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:56,175 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:32:56,175 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:56,176 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:56,176 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:56,176 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:56,176 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:56,176 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:56,176 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:56,177 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:56,177 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:56,177 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:56,177 #include "..." search starts here: 2025-09-09T00:32:56,177 #include <...> search starts here: 2025-09-09T00:32:56,177 /usr/include/eigen3 2025-09-09T00:32:56,177 include 2025-09-09T00:32:56,177 /usr/include/python3.13 2025-09-09T00:32:56,178 /usr/include/c++/14 2025-09-09T00:32:56,178 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:56,178 /usr/include/c++/14/backward 2025-09-09T00:32:56,178 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:56,178 /usr/local/include 2025-09-09T00:32:56,178 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:56,178 /usr/include 2025-09-09T00:32:56,179 End of search list. 2025-09-09T00:32:56,195 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:57,445 In file included from ./src/base.cpp:21: 2025-09-09T00:32:57,446 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:57,446 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:57,446 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:57,446 | ^ 2025-09-09T00:32:57,446 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:57,446 37 | # define UNUSED(x) x 2025-09-09T00:32:57,446 | ^ 2025-09-09T00:32:58,620 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/base.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:58,620 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/base.o /tmp/cc92cpEW.s 2025-09-09T00:32:58,625 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:58,745 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:32:58,745 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:32:58,745 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/base.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/base.' 2025-09-09T00:32:58,745 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/bitvec.cpp -o build/temp.linux-armv7l-cpython-313/src/bitvec.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:32:58,749 Using built-in specs. 2025-09-09T00:32:58,750 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:58,750 Target: arm-linux-gnueabihf 2025-09-09T00:32:58,750 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:32:58,750 Thread model: posix 2025-09-09T00:32:58,750 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:58,750 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:58,750 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bitvec.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:32:58,751 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/bitvec.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase bitvec.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccw7kzKE.s 2025-09-09T00:32:58,760 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:58,760 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:32:58,760 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:58,761 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:58,761 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:58,761 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:58,761 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:58,761 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:58,761 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:58,761 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:58,761 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:58,762 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:58,762 #include "..." search starts here: 2025-09-09T00:32:58,762 #include <...> search starts here: 2025-09-09T00:32:58,762 /usr/include/eigen3 2025-09-09T00:32:58,762 include 2025-09-09T00:32:58,762 /usr/include/python3.13 2025-09-09T00:32:58,762 /usr/include/c++/14 2025-09-09T00:32:58,762 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:58,763 /usr/include/c++/14/backward 2025-09-09T00:32:58,763 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:58,763 /usr/local/include 2025-09-09T00:32:58,763 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:58,763 /usr/include 2025-09-09T00:32:58,763 End of search list. 2025-09-09T00:32:58,780 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:02,796 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bitvec.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:02,796 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/bitvec.o /tmp/ccw7kzKE.s 2025-09-09T00:33:02,802 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:03,074 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:33:03,074 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:33:03,074 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bitvec.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/bitvec.' 2025-09-09T00:33:03,076 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/bond.cpp -o build/temp.linux-armv7l-cpython-313/src/bond.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:33:03,080 Using built-in specs. 2025-09-09T00:33:03,081 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:03,081 Target: arm-linux-gnueabihf 2025-09-09T00:33:03,081 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:33:03,081 Thread model: posix 2025-09-09T00:33:03,081 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:03,081 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:03,081 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bond.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:03,081 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/bond.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase bond.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cctppZoG.s 2025-09-09T00:33:03,091 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:03,091 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:33:03,091 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:03,091 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:03,092 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:03,092 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:03,092 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:03,092 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:03,092 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:03,092 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:03,092 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:03,093 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:03,093 #include "..." search starts here: 2025-09-09T00:33:03,093 #include <...> search starts here: 2025-09-09T00:33:03,093 /usr/include/eigen3 2025-09-09T00:33:03,093 include 2025-09-09T00:33:03,093 /usr/include/python3.13 2025-09-09T00:33:03,093 /usr/include/c++/14 2025-09-09T00:33:03,093 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:03,094 /usr/include/c++/14/backward 2025-09-09T00:33:03,094 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:03,094 /usr/local/include 2025-09-09T00:33:03,094 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:03,094 /usr/include 2025-09-09T00:33:03,094 End of search list. 2025-09-09T00:33:03,112 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:04,515 In file included from include/openbabel/bond.h:31, 2025-09-09T00:33:04,515 from ./src/bond.cpp:21: 2025-09-09T00:33:04,515 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:04,515 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:04,515 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:04,515 | ^ 2025-09-09T00:33:04,515 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:04,516 37 | # define UNUSED(x) x 2025-09-09T00:33:04,516 | ^ 2025-09-09T00:33:05,199 In file included from include/openbabel/mol.h:52, 2025-09-09T00:33:05,199 from ./src/bond.cpp:22: 2025-09-09T00:33:05,200 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,200 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,200 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:05,200 | ^ 2025-09-09T00:33:05,200 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:05,200 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:05,200 | ^~~~~~~~ 2025-09-09T00:33:05,203 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,203 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,203 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:05,204 | ^ 2025-09-09T00:33:05,204 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:05,204 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:05,204 | ^~~~~~~~ 2025-09-09T00:33:05,218 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,218 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,218 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:05,218 | ^ 2025-09-09T00:33:05,218 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:05,218 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:05,218 | ^~~~~~~~ 2025-09-09T00:33:05,222 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,223 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,223 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:05,223 | ^ 2025-09-09T00:33:05,223 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:05,223 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:05,223 | ^~~~~~~~ 2025-09-09T00:33:07,917 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bond.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:07,917 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/bond.o /tmp/cctppZoG.s 2025-09-09T00:33:07,922 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:08,138 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:33:08,139 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:33:08,139 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bond.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/bond.' 2025-09-09T00:33:08,141 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/bondtyper.cpp -o build/temp.linux-armv7l-cpython-313/src/bondtyper.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:33:08,144 Using built-in specs. 2025-09-09T00:33:08,145 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:08,145 Target: arm-linux-gnueabihf 2025-09-09T00:33:08,145 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:33:08,146 Thread model: posix 2025-09-09T00:33:08,146 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:08,146 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:08,146 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bondtyper.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:08,146 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/bondtyper.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase bondtyper.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccXPLCGo.s 2025-09-09T00:33:08,157 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:08,157 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:33:08,157 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:08,157 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:08,157 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:08,157 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:08,157 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:08,158 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:08,158 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:08,158 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:08,158 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:08,158 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:08,158 #include "..." search starts here: 2025-09-09T00:33:08,158 #include <...> search starts here: 2025-09-09T00:33:08,158 /usr/include/eigen3 2025-09-09T00:33:08,158 include 2025-09-09T00:33:08,158 /usr/include/python3.13 2025-09-09T00:33:08,159 /usr/include/c++/14 2025-09-09T00:33:08,159 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:08,159 /usr/include/c++/14/backward 2025-09-09T00:33:08,159 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:08,159 /usr/local/include 2025-09-09T00:33:08,159 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:08,159 /usr/include 2025-09-09T00:33:08,159 End of search list. 2025-09-09T00:33:08,173 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:09,645 In file included from include/openbabel/atom.h:33, 2025-09-09T00:33:09,645 from include/openbabel/mol.h:43, 2025-09-09T00:33:09,646 from ./src/bondtyper.cpp:20: 2025-09-09T00:33:09,646 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:09,646 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:09,646 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:09,646 | ^ 2025-09-09T00:33:09,646 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:09,646 37 | # define UNUSED(x) x 2025-09-09T00:33:09,646 | ^ 2025-09-09T00:33:10,256 In file included from include/openbabel/mol.h:52: 2025-09-09T00:33:10,256 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:10,256 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:10,256 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:10,256 | ^ 2025-09-09T00:33:10,256 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:10,256 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:10,257 | ^~~~~~~~ 2025-09-09T00:33:10,260 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:10,260 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:10,260 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:10,260 | ^ 2025-09-09T00:33:10,260 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:10,260 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:10,260 | ^~~~~~~~ 2025-09-09T00:33:10,274 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:10,274 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:10,274 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:10,274 | ^ 2025-09-09T00:33:10,275 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:10,275 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:10,275 | ^~~~~~~~ 2025-09-09T00:33:10,279 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:10,279 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:10,279 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:10,279 | ^ 2025-09-09T00:33:10,279 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:10,280 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:10,280 | ^~~~~~~~ 2025-09-09T00:33:13,421 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bondtyper.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:13,422 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/bondtyper.o /tmp/ccXPLCGo.s 2025-09-09T00:33:13,426 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:13,671 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:33:13,671 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:33:13,671 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/bondtyper.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/bondtyper.' 2025-09-09T00:33:13,673 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/builder.cpp -o build/temp.linux-armv7l-cpython-313/src/builder.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:33:13,678 Using built-in specs. 2025-09-09T00:33:13,678 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:13,678 Target: arm-linux-gnueabihf 2025-09-09T00:33:13,678 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:33:13,678 Thread model: posix 2025-09-09T00:33:13,679 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:13,679 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:13,679 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/builder.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:13,679 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/builder.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase builder.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccaymSts.s 2025-09-09T00:33:13,690 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:13,690 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:33:13,690 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:13,690 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:13,690 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:13,690 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:13,690 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:13,691 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:13,691 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:13,691 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:13,691 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:13,691 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:13,691 #include "..." search starts here: 2025-09-09T00:33:13,691 #include <...> search starts here: 2025-09-09T00:33:13,691 /usr/include/eigen3 2025-09-09T00:33:13,691 include 2025-09-09T00:33:13,692 /usr/include/python3.13 2025-09-09T00:33:13,692 /usr/include/c++/14 2025-09-09T00:33:13,692 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:13,692 /usr/include/c++/14/backward 2025-09-09T00:33:13,692 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:13,692 /usr/local/include 2025-09-09T00:33:13,692 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:13,692 /usr/include 2025-09-09T00:33:13,692 End of search list. 2025-09-09T00:33:13,710 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:14,582 ./src/builder.cpp:188:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:33:14,582 188 | // \ \ 2025-09-09T00:33:14,582 | ^ 2025-09-09T00:33:14,583 ./src/builder.cpp:190:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:33:14,583 190 | // \ 2025-09-09T00:33:14,583 | ^ 2025-09-09T00:33:14,583 ./src/builder.cpp:197:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:33:14,583 197 | // \ \ 2025-09-09T00:33:14,583 | ^ 2025-09-09T00:33:14,584 ./src/builder.cpp:199:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:33:14,584 199 | // \ 2025-09-09T00:33:14,584 | ^ 2025-09-09T00:33:14,585 ./src/builder.cpp:265:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:33:14,585 265 | // \ \ 2025-09-09T00:33:14,585 | ^ 2025-09-09T00:33:14,591 ./src/builder.cpp:1215:5: warning: multi-line comment [-Wcomment] 2025-09-09T00:33:14,591 1215 | // / / v2 / \ 2025-09-09T00:33:14,591 | ^ 2025-09-09T00:33:14,593 ./src/builder.cpp:1324:9: warning: multi-line comment [-Wcomment] 2025-09-09T00:33:14,594 1324 | // / \ 2025-09-09T00:33:14,594 | ^ 2025-09-09T00:33:15,623 In file included from include/openbabel/builder.h:29, 2025-09-09T00:33:15,624 from ./src/builder.cpp:22: 2025-09-09T00:33:15,624 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:15,624 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:15,624 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:15,624 | ^ 2025-09-09T00:33:15,624 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:15,624 37 | # define UNUSED(x) x 2025-09-09T00:33:15,624 | ^ 2025-09-09T00:33:16,256 In file included from include/openbabel/mol.h:52, 2025-09-09T00:33:16,256 from include/openbabel/builder.h:30: 2025-09-09T00:33:16,257 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:16,257 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:16,257 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:16,257 | ^ 2025-09-09T00:33:16,257 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:16,257 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:16,257 | ^~~~~~~~ 2025-09-09T00:33:16,261 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:16,262 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:16,262 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:16,262 | ^ 2025-09-09T00:33:16,262 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:16,262 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:16,262 | ^~~~~~~~ 2025-09-09T00:33:16,277 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:16,277 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:16,277 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:16,277 | ^ 2025-09-09T00:33:16,277 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:16,277 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:16,278 | ^~~~~~~~ 2025-09-09T00:33:16,283 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:16,283 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:16,283 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:16,283 | ^ 2025-09-09T00:33:16,283 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:16,283 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:16,283 | ^~~~~~~~ 2025-09-09T00:33:16,532 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:33:16,532 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:33:16,532 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:33:16,532 | ^ 2025-09-09T00:33:16,532 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:16,532 37 | # define UNUSED(x) x 2025-09-09T00:33:16,532 | ^ 2025-09-09T00:33:16,533 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:33:16,533 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:33:16,533 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:33:16,533 | ^ 2025-09-09T00:33:16,534 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:16,534 37 | # define UNUSED(x) x 2025-09-09T00:33:16,534 | ^ 2025-09-09T00:33:16,598 In file included from include/openbabel/format.h:22, 2025-09-09T00:33:16,598 from include/openbabel/obconversion.h:37, 2025-09-09T00:33:16,598 from ./src/builder.cpp:31: 2025-09-09T00:33:16,598 include/openbabel/plugin.h: At global scope: 2025-09-09T00:33:16,598 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:33:16,598 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:33:16,598 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:16,599 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:33:16,599 from /usr/include/c++/14/vector:68, 2025-09-09T00:33:16,600 from include/openbabel/builder.h:23: 2025-09-09T00:33:16,600 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:33:16,600 131 | struct binary_function 2025-09-09T00:33:16,600 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:28,708 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/builder.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:28,709 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/builder.o /tmp/ccaymSts.s 2025-09-09T00:33:28,713 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:29,574 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:33:29,575 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:33:29,575 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/builder.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/builder.' 2025-09-09T00:33:29,577 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/canon.cpp -o build/temp.linux-armv7l-cpython-313/src/canon.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:33:29,582 Using built-in specs. 2025-09-09T00:33:29,583 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:29,583 Target: arm-linux-gnueabihf 2025-09-09T00:33:29,583 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:33:29,583 Thread model: posix 2025-09-09T00:33:29,584 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:29,584 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:29,584 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/canon.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:29,584 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/canon.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase canon.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccjqTKCe.s 2025-09-09T00:33:29,595 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:29,596 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:33:29,596 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:29,596 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:29,597 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:29,597 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:29,597 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:29,597 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:29,597 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:29,597 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:29,598 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:29,598 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:29,598 #include "..." search starts here: 2025-09-09T00:33:29,598 #include <...> search starts here: 2025-09-09T00:33:29,598 /usr/include/eigen3 2025-09-09T00:33:29,598 include 2025-09-09T00:33:29,598 /usr/include/python3.13 2025-09-09T00:33:29,599 /usr/include/c++/14 2025-09-09T00:33:29,599 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:29,599 /usr/include/c++/14/backward 2025-09-09T00:33:29,599 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:29,599 /usr/local/include 2025-09-09T00:33:29,599 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:29,599 /usr/include 2025-09-09T00:33:29,600 End of search list. 2025-09-09T00:33:29,616 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:31,062 In file included from include/openbabel/stereo/stereo.h:27, 2025-09-09T00:33:31,062 from include/openbabel/graphsym.h:25, 2025-09-09T00:33:31,062 from ./src/canon.cpp:22: 2025-09-09T00:33:31,062 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:31,063 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:31,063 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:31,063 | ^ 2025-09-09T00:33:31,063 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:31,063 37 | # define UNUSED(x) x 2025-09-09T00:33:31,063 | ^ 2025-09-09T00:33:31,712 In file included from include/openbabel/mol.h:52, 2025-09-09T00:33:31,712 from include/openbabel/isomorphism.h:27, 2025-09-09T00:33:31,712 from include/openbabel/stereo/stereo.h:28: 2025-09-09T00:33:31,712 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:31,712 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:31,712 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:31,712 | ^ 2025-09-09T00:33:31,713 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:31,713 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:31,713 | ^~~~~~~~ 2025-09-09T00:33:31,716 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:31,716 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:31,716 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:31,716 | ^ 2025-09-09T00:33:31,716 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:31,716 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:31,716 | ^~~~~~~~ 2025-09-09T00:33:31,730 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:31,730 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:31,730 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:31,730 | ^ 2025-09-09T00:33:31,730 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:31,731 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:31,731 | ^~~~~~~~ 2025-09-09T00:33:31,735 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:31,735 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:31,735 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:31,735 | ^ 2025-09-09T00:33:31,735 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:31,736 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:31,736 | ^~~~~~~~ 2025-09-09T00:33:32,092 ./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)’: 2025-09-09T00:33:32,092 ./src/canon.cpp:708:34: warning: ‘OpenBabel::CanonicalLabelsImpl::State::stereoCenters’ will be initialized after [-Wreorder] 2025-09-09T00:33:32,092 708 | std::vector &stereoCenters; 2025-09-09T00:33:32,092 | ^~~~~~~~~~~~~ 2025-09-09T00:33:32,092 ./src/canon.cpp:702:18: warning: ‘const bool OpenBabel::CanonicalLabelsImpl::State::onlyOne’ [-Wreorder] 2025-09-09T00:33:32,092 702 | const bool onlyOne; 2025-09-09T00:33:32,093 | ^~~~~~~ 2025-09-09T00:33:32,093 ./src/canon.cpp:683:7: warning: when initialized here [-Wreorder] 2025-09-09T00:33:32,093 683 | State(const std::vector &_symmetry_classes, 2025-09-09T00:33:32,093 | ^~~~~ 2025-09-09T00:33:32,171 ./src/canon.cpp: In static member function ‘static void OpenBabel::CanonicalLabelsImpl::UpdateMcr(OpenBabel::OBBitVec&, Orbits&, OpenBabel::OBMol*, const std::vector&)’: 2025-09-09T00:33:32,172 ./src/canon.cpp:1134:65: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:33:32,172 1134 | static void UpdateMcr(OBBitVec &mcr, Orbits &orbits, OBMol *mol, const std::vector &bestLabels) 2025-09-09T00:33:32,172 | ~~~~~~~^~~ 2025-09-09T00:33:50,681 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/canon.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:50,682 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/canon.o /tmp/ccjqTKCe.s 2025-09-09T00:33:50,687 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:52,376 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:33:52,376 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:33:52,376 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/canon.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/canon.' 2025-09-09T00:33:52,381 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/chains.cpp -o build/temp.linux-armv7l-cpython-313/src/chains.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:33:52,385 Using built-in specs. 2025-09-09T00:33:52,386 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:52,386 Target: arm-linux-gnueabihf 2025-09-09T00:33:52,387 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:33:52,387 Thread model: posix 2025-09-09T00:33:52,387 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:52,387 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:52,387 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chains.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:33:52,387 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/chains.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase chains.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccnQK6K4.s 2025-09-09T00:33:52,398 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:52,398 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:33:52,398 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:52,398 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:52,398 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:52,399 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:52,399 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:52,399 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:52,399 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:52,399 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:52,399 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:52,399 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:52,400 #include "..." search starts here: 2025-09-09T00:33:52,400 #include <...> search starts here: 2025-09-09T00:33:52,400 /usr/include/eigen3 2025-09-09T00:33:52,400 include 2025-09-09T00:33:52,400 /usr/include/python3.13 2025-09-09T00:33:52,400 /usr/include/c++/14 2025-09-09T00:33:52,400 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:52,400 /usr/include/c++/14/backward 2025-09-09T00:33:52,400 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:52,401 /usr/local/include 2025-09-09T00:33:52,401 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:52,401 /usr/include 2025-09-09T00:33:52,401 End of search list. 2025-09-09T00:33:52,418 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:53,902 In file included from include/openbabel/atom.h:33, 2025-09-09T00:33:53,902 from include/openbabel/mol.h:43, 2025-09-09T00:33:53,902 from ./src/chains.cpp:33: 2025-09-09T00:33:53,902 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:53,903 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:53,903 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:53,903 | ^ 2025-09-09T00:33:53,903 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:53,903 37 | # define UNUSED(x) x 2025-09-09T00:33:53,903 | ^ 2025-09-09T00:33:54,509 In file included from include/openbabel/mol.h:52: 2025-09-09T00:33:54,510 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:54,510 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:54,510 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:54,510 | ^ 2025-09-09T00:33:54,510 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:54,510 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:54,510 | ^~~~~~~~ 2025-09-09T00:33:54,513 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:54,513 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:54,514 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:54,514 | ^ 2025-09-09T00:33:54,514 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:54,514 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:54,514 | ^~~~~~~~ 2025-09-09T00:33:54,528 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:54,528 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:54,528 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:54,528 | ^ 2025-09-09T00:33:54,528 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:54,528 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:54,528 | ^~~~~~~~ 2025-09-09T00:33:54,533 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:54,533 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:54,533 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:54,533 | ^ 2025-09-09T00:33:54,533 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:54,533 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:54,533 | ^~~~~~~~ 2025-09-09T00:33:59,065 ./src/chains.cpp: In member function ‘void OpenBabel::OBChainsParser::ConstrainBackbone(OpenBabel::OBMol&, OpenBabel::Template*, int)’: 2025-09-09T00:33:59,065 ./src/chains.cpp:1275:51: warning: ‘nb’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:33:59,065 1275 | result = Match2Constraints(pep,na,nb); 2025-09-09T00:33:59,065 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:33:59,065 ./src/chains.cpp:1219:17: note: ‘nb’ was declared here 2025-09-09T00:33:59,065 1219 | OBAtom *na,*nb,*nc,*nd; 2025-09-09T00:33:59,065 | ^~ 2025-09-09T00:33:59,066 ./src/chains.cpp:1277:49: warning: ‘na’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:33:59,066 1277 | result = MatchConstraint(na,pep->n1); 2025-09-09T00:33:59,066 | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T00:33:59,066 ./src/chains.cpp:1219:13: note: ‘na’ was declared here 2025-09-09T00:33:59,066 1219 | OBAtom *na,*nb,*nc,*nd; 2025-09-09T00:33:59,066 | ^~ 2025-09-09T00:34:03,211 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chains.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:34:03,211 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/chains.o /tmp/ccnQK6K4.s 2025-09-09T00:34:03,218 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:03,847 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:34:03,847 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:34:03,847 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chains.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/chains.' 2025-09-09T00:34:03,850 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/chargemodel.cpp -o build/temp.linux-armv7l-cpython-313/src/chargemodel.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:34:03,854 Using built-in specs. 2025-09-09T00:34:03,855 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:03,855 Target: arm-linux-gnueabihf 2025-09-09T00:34:03,855 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:34:03,855 Thread model: posix 2025-09-09T00:34:03,855 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:03,855 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:03,855 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chargemodel.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:34:03,855 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/chargemodel.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase chargemodel.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccZpo099.s 2025-09-09T00:34:03,865 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:03,866 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:34:03,866 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:03,866 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:03,866 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:03,866 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:03,866 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:03,866 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:03,867 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:03,867 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:03,867 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:03,867 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:03,867 #include "..." search starts here: 2025-09-09T00:34:03,867 #include <...> search starts here: 2025-09-09T00:34:03,867 /usr/include/eigen3 2025-09-09T00:34:03,867 include 2025-09-09T00:34:03,867 /usr/include/python3.13 2025-09-09T00:34:03,867 /usr/include/c++/14 2025-09-09T00:34:03,868 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:03,868 /usr/include/c++/14/backward 2025-09-09T00:34:03,868 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:03,868 /usr/local/include 2025-09-09T00:34:03,868 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:03,868 /usr/include 2025-09-09T00:34:03,868 End of search list. 2025-09-09T00:34:03,883 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:05,184 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:05,184 from ./src/chargemodel.cpp:21: 2025-09-09T00:34:05,184 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:05,184 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:05,184 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:05,184 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:05,185 from include/openbabel/plugin.h:23: 2025-09-09T00:34:05,185 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:05,185 131 | struct binary_function 2025-09-09T00:34:05,185 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:05,294 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:05,294 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:05,294 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:05,294 | ~~~~~~~^ 2025-09-09T00:34:05,294 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:05,295 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:05,295 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:05,295 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:05,394 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:05,394 from include/openbabel/mol.h:43, 2025-09-09T00:34:05,395 from ./src/chargemodel.cpp:22: 2025-09-09T00:34:05,395 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:05,395 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:05,395 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:05,395 | ^ 2025-09-09T00:34:05,395 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:05,395 37 | # define UNUSED(x) x 2025-09-09T00:34:05,395 | ^ 2025-09-09T00:34:05,984 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:05,984 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:05,984 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:05,984 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:05,984 | ^ 2025-09-09T00:34:05,984 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:05,984 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:05,984 | ^~~~~~~~ 2025-09-09T00:34:05,987 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:05,988 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:05,988 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:05,988 | ^ 2025-09-09T00:34:05,988 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:05,988 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:05,988 | ^~~~~~~~ 2025-09-09T00:34:06,002 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:06,002 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:06,002 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:06,002 | ^ 2025-09-09T00:34:06,002 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:06,002 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:06,003 | ^~~~~~~~ 2025-09-09T00:34:06,007 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:06,007 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:06,007 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:06,007 | ^ 2025-09-09T00:34:06,007 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:06,007 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:06,007 | ^~~~~~~~ 2025-09-09T00:34:07,416 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chargemodel.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:34:07,416 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/chargemodel.o /tmp/ccZpo099.s 2025-09-09T00:34:07,421 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:07,477 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:34:07,477 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:34:07,478 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chargemodel.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/chargemodel.' 2025-09-09T00:34:07,478 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/eem.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/eem.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:34:07,483 Using built-in specs. 2025-09-09T00:34:07,484 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:07,484 Target: arm-linux-gnueabihf 2025-09-09T00:34:07,484 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:34:07,484 Thread model: posix 2025-09-09T00:34:07,484 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:07,484 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:07,484 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/eem.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:07,485 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/eem.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase eem.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccXSKO31.s 2025-09-09T00:34:07,497 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:07,497 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:34:07,497 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:07,497 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:07,497 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:07,498 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:07,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:07,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:07,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:07,498 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:07,498 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:07,499 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:07,499 #include "..." search starts here: 2025-09-09T00:34:07,499 #include <...> search starts here: 2025-09-09T00:34:07,499 /usr/include/eigen3 2025-09-09T00:34:07,499 include 2025-09-09T00:34:07,499 /usr/include/python3.13 2025-09-09T00:34:07,499 /usr/include/c++/14 2025-09-09T00:34:07,500 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:07,500 /usr/include/c++/14/backward 2025-09-09T00:34:07,500 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:07,500 /usr/local/include 2025-09-09T00:34:07,500 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:07,500 /usr/include 2025-09-09T00:34:07,500 End of search list. 2025-09-09T00:34:07,516 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:08,818 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:08,818 from ./src/charges/eem.cpp:23: 2025-09-09T00:34:08,818 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:08,818 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:08,818 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:08,818 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:08,818 from ./src/charges/eem.cpp:19: 2025-09-09T00:34:08,818 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:08,819 131 | struct binary_function 2025-09-09T00:34:08,819 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:08,927 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:08,928 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:08,928 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:08,928 | ~~~~~~~^ 2025-09-09T00:34:08,928 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:08,928 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:08,928 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:08,928 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:09,029 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:09,029 from include/openbabel/mol.h:43, 2025-09-09T00:34:09,029 from ./src/charges/eem.cpp:24: 2025-09-09T00:34:09,029 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:09,030 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:09,030 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:09,030 | ^ 2025-09-09T00:34:09,030 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:09,030 37 | # define UNUSED(x) x 2025-09-09T00:34:09,030 | ^ 2025-09-09T00:34:09,623 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:09,623 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:09,624 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:09,624 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:09,624 | ^ 2025-09-09T00:34:09,624 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:09,624 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:09,624 | ^~~~~~~~ 2025-09-09T00:34:09,627 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:09,627 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:09,627 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:09,628 | ^ 2025-09-09T00:34:09,628 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:09,628 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:09,628 | ^~~~~~~~ 2025-09-09T00:34:09,642 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:09,642 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:09,642 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:09,642 | ^ 2025-09-09T00:34:09,642 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:09,642 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:09,642 | ^~~~~~~~ 2025-09-09T00:34:09,646 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:09,647 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:09,647 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:09,647 | ^ 2025-09-09T00:34:09,647 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:09,647 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:09,647 | ^~~~~~~~ 2025-09-09T00:34:13,343 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/eem.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:13,343 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/eem.o /tmp/ccXSKO31.s 2025-09-09T00:34:13,348 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:13,638 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:34:13,639 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:34:13,639 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/eem.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/eem.' 2025-09-09T00:34:13,641 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/eqeq.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/eqeq.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:34:13,645 Using built-in specs. 2025-09-09T00:34:13,645 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:13,645 Target: arm-linux-gnueabihf 2025-09-09T00:34:13,646 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:34:13,646 Thread model: posix 2025-09-09T00:34:13,646 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:13,646 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:13,646 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/eqeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:13,646 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/eqeq.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase eqeq.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccB7YpFS.s 2025-09-09T00:34:13,657 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:13,657 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:34:13,657 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:13,657 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:13,658 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:13,658 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:13,658 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:13,658 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:13,658 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:13,658 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:13,658 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:13,659 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:13,659 #include "..." search starts here: 2025-09-09T00:34:13,659 #include <...> search starts here: 2025-09-09T00:34:13,659 /usr/include/eigen3 2025-09-09T00:34:13,659 include 2025-09-09T00:34:13,659 /usr/include/python3.13 2025-09-09T00:34:13,659 /usr/include/c++/14 2025-09-09T00:34:13,659 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:13,660 /usr/include/c++/14/backward 2025-09-09T00:34:13,660 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:13,660 /usr/local/include 2025-09-09T00:34:13,660 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:13,660 /usr/include 2025-09-09T00:34:13,660 End of search list. 2025-09-09T00:34:13,677 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:15,378 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:15,378 from include/charges/eqeq.h:22, 2025-09-09T00:34:15,378 from ./src/charges/eqeq.cpp:19: 2025-09-09T00:34:15,378 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:15,378 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:15,378 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:15,379 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:15,379 from include/openbabel/plugin.h:23: 2025-09-09T00:34:15,379 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:15,379 131 | struct binary_function 2025-09-09T00:34:15,379 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:15,485 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:15,485 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:15,485 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:15,486 | ~~~~~~~^ 2025-09-09T00:34:15,486 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:15,486 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:15,486 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:15,486 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:15,588 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:15,588 from include/openbabel/mol.h:43, 2025-09-09T00:34:15,588 from include/charges/eqeq.h:23: 2025-09-09T00:34:15,588 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:15,588 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:15,588 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:15,589 | ^ 2025-09-09T00:34:15,589 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:15,589 37 | # define UNUSED(x) x 2025-09-09T00:34:15,589 | ^ 2025-09-09T00:34:16,177 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:16,177 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:16,178 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:16,178 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:16,178 | ^ 2025-09-09T00:34:16,178 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:16,178 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:16,178 | ^~~~~~~~ 2025-09-09T00:34:16,181 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:16,181 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:16,182 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:16,182 | ^ 2025-09-09T00:34:16,182 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:16,182 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:16,182 | ^~~~~~~~ 2025-09-09T00:34:16,196 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:16,196 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:16,196 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:16,196 | ^ 2025-09-09T00:34:16,196 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:16,196 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:16,197 | ^~~~~~~~ 2025-09-09T00:34:16,201 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:16,201 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:16,201 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:16,201 | ^ 2025-09-09T00:34:16,201 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:16,201 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:16,202 | ^~~~~~~~ 2025-09-09T00:34:38,727 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/eqeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:38,728 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/eqeq.o /tmp/ccB7YpFS.s 2025-09-09T00:34:38,735 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:40,872 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:34:40,872 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:34:40,873 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/eqeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/eqeq.' 2025-09-09T00:34:40,882 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/fromfile.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/fromfile.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:34:40,887 Using built-in specs. 2025-09-09T00:34:40,887 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:40,888 Target: arm-linux-gnueabihf 2025-09-09T00:34:40,888 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:34:40,888 Thread model: posix 2025-09-09T00:34:40,888 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:40,888 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:40,888 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/fromfile.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:40,888 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/fromfile.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase fromfile.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccLlvBU7.s 2025-09-09T00:34:40,901 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:40,901 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:34:40,901 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:40,901 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:40,902 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:40,902 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:40,902 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:40,902 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:40,903 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:40,903 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:40,903 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:40,903 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:40,903 #include "..." search starts here: 2025-09-09T00:34:40,903 #include <...> search starts here: 2025-09-09T00:34:40,903 /usr/include/eigen3 2025-09-09T00:34:40,903 include 2025-09-09T00:34:40,904 /usr/include/python3.13 2025-09-09T00:34:40,904 /usr/include/c++/14 2025-09-09T00:34:40,904 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:40,904 /usr/include/c++/14/backward 2025-09-09T00:34:40,904 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:40,904 /usr/local/include 2025-09-09T00:34:40,904 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:40,904 /usr/include 2025-09-09T00:34:40,905 End of search list. 2025-09-09T00:34:40,919 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:42,257 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:42,257 from ./src/charges/fromfile.cpp:21: 2025-09-09T00:34:42,257 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:42,257 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:42,257 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:42,257 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:42,257 from include/openbabel/plugin.h:23: 2025-09-09T00:34:42,258 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:42,258 131 | struct binary_function 2025-09-09T00:34:42,258 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:42,366 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:42,366 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:42,367 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:42,367 | ~~~~~~~^ 2025-09-09T00:34:42,367 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:42,367 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:42,367 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:42,367 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:42,468 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:42,468 from include/openbabel/mol.h:43, 2025-09-09T00:34:42,468 from ./src/charges/fromfile.cpp:22: 2025-09-09T00:34:42,468 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:42,468 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:42,468 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:42,468 | ^ 2025-09-09T00:34:42,469 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:42,469 37 | # define UNUSED(x) x 2025-09-09T00:34:42,469 | ^ 2025-09-09T00:34:43,064 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:43,064 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:43,064 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:43,064 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:43,065 | ^ 2025-09-09T00:34:43,065 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:43,065 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:43,065 | ^~~~~~~~ 2025-09-09T00:34:43,068 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:43,068 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:43,068 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:43,068 | ^ 2025-09-09T00:34:43,068 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:43,069 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:43,069 | ^~~~~~~~ 2025-09-09T00:34:43,082 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:43,083 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:43,083 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:43,083 | ^ 2025-09-09T00:34:43,083 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:43,083 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:43,083 | ^~~~~~~~ 2025-09-09T00:34:43,087 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:43,087 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:43,088 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:43,088 | ^ 2025-09-09T00:34:43,088 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:43,088 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:43,088 | ^~~~~~~~ 2025-09-09T00:34:43,425 ./src/charges/fromfile.cpp: In member function ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:43,426 ./src/charges/fromfile.cpp:96:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:34:43,426 96 | for ( int i = 1; i <= mol.NumAtoms(); i++) 2025-09-09T00:34:43,426 | ~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:34:45,576 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:34:45,576 from include/openbabel/plugin.h:26: 2025-09-09T00:34:45,576 /usr/include/c++/14/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> >]’: 2025-09-09T00:34:45,576 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-09T00:34:45,576 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:34:45,576 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,286 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:34:46,286 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> >]’, 2025-09-09T00:34:46,286 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:112:32: 2025-09-09T00:34:46,287 /usr/include/c++/14/bits/stl_map.h:532:44: 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 2025-09-09T00:34:46,287 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:34:46,287 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,287 533 | std::forward_as_tuple(std::move(__k)), 2025-09-09T00:34:46,287 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,287 534 | std::tuple<>()); 2025-09-09T00:34:46,287 | ~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,288 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> >]’, 2025-09-09T00:34:46,288 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:120:32: 2025-09-09T00:34:46,288 /usr/include/c++/14/bits/stl_map.h:532:44: 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 2025-09-09T00:34:46,289 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:34:46,289 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,289 533 | std::forward_as_tuple(std::move(__k)), 2025-09-09T00:34:46,289 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,289 534 | std::tuple<>()); 2025-09-09T00:34:46,289 | ~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,290 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> >]’, 2025-09-09T00:34:46,290 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:128:32: 2025-09-09T00:34:46,290 /usr/include/c++/14/bits/stl_map.h:532:44: 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 2025-09-09T00:34:46,290 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:34:46,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,290 533 | std::forward_as_tuple(std::move(__k)), 2025-09-09T00:34:46,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:34:46,291 534 | std::tuple<>()); 2025-09-09T00:34:46,291 | ~~~~~~~~~~~~~~~ 2025-09-09T00:34:47,218 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/fromfile.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:47,219 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/fromfile.o /tmp/ccLlvBU7.s 2025-09-09T00:34:47,224 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:47,549 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:34:47,550 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:34:47,550 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/fromfile.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/fromfile.' 2025-09-09T00:34:47,552 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/gasteiger.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/gasteiger.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:34:47,556 Using built-in specs. 2025-09-09T00:34:47,556 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:47,556 Target: arm-linux-gnueabihf 2025-09-09T00:34:47,557 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:34:47,557 Thread model: posix 2025-09-09T00:34:47,557 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:47,557 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:47,557 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/gasteiger.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:47,557 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/gasteiger.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase gasteiger.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccjEuBqQ.s 2025-09-09T00:34:47,569 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:47,569 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:34:47,569 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:47,569 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:47,569 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:47,570 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:47,570 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:47,570 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:47,570 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:47,570 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:47,571 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:47,571 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:47,571 #include "..." search starts here: 2025-09-09T00:34:47,571 #include <...> search starts here: 2025-09-09T00:34:47,571 /usr/include/eigen3 2025-09-09T00:34:47,571 include 2025-09-09T00:34:47,571 /usr/include/python3.13 2025-09-09T00:34:47,571 /usr/include/c++/14 2025-09-09T00:34:47,572 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:47,572 /usr/include/c++/14/backward 2025-09-09T00:34:47,572 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:47,572 /usr/local/include 2025-09-09T00:34:47,572 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:47,572 /usr/include 2025-09-09T00:34:47,572 End of search list. 2025-09-09T00:34:47,588 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:48,892 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:48,892 from ./src/charges/gasteiger.cpp:20: 2025-09-09T00:34:48,892 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:48,892 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:48,892 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:48,893 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:48,893 from include/openbabel/plugin.h:23: 2025-09-09T00:34:48,893 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:48,893 131 | struct binary_function 2025-09-09T00:34:48,893 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:49,001 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:49,001 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:49,001 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:49,002 | ~~~~~~~^ 2025-09-09T00:34:49,002 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:49,002 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:49,002 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:49,002 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:49,103 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:49,103 from include/openbabel/mol.h:43, 2025-09-09T00:34:49,103 from ./src/charges/gasteiger.cpp:21: 2025-09-09T00:34:49,103 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:49,104 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:49,104 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:49,104 | ^ 2025-09-09T00:34:49,104 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:49,104 37 | # define UNUSED(x) x 2025-09-09T00:34:49,104 | ^ 2025-09-09T00:34:49,691 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:49,691 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:49,691 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:49,691 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:49,691 | ^ 2025-09-09T00:34:49,691 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:49,691 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:49,692 | ^~~~~~~~ 2025-09-09T00:34:49,695 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:49,695 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:49,695 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:49,695 | ^ 2025-09-09T00:34:49,695 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:49,695 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:49,695 | ^~~~~~~~ 2025-09-09T00:34:49,709 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:49,709 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:49,709 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:49,709 | ^ 2025-09-09T00:34:49,710 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:49,710 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:49,710 | ^~~~~~~~ 2025-09-09T00:34:49,714 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:49,714 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:49,714 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:49,714 | ^ 2025-09-09T00:34:49,714 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:49,715 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:49,715 | ^~~~~~~~ 2025-09-09T00:34:51,613 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/gasteiger.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:51,613 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/gasteiger.o /tmp/ccjEuBqQ.s 2025-09-09T00:34:51,618 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:51,737 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:34:51,737 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:34:51,737 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/gasteiger.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/gasteiger.' 2025-09-09T00:34:51,738 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/mmff94.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/mmff94.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:34:51,742 Using built-in specs. 2025-09-09T00:34:51,743 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:51,743 Target: arm-linux-gnueabihf 2025-09-09T00:34:51,743 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:34:51,743 Thread model: posix 2025-09-09T00:34:51,743 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:51,744 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:51,744 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/mmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:51,744 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/mmff94.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase mmff94.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc8vJyut.s 2025-09-09T00:34:51,756 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:51,756 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:34:51,756 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:51,756 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:51,757 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:51,757 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:51,757 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:51,757 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:51,757 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:51,758 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:51,758 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:51,758 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:51,758 #include "..." search starts here: 2025-09-09T00:34:51,758 #include <...> search starts here: 2025-09-09T00:34:51,758 /usr/include/eigen3 2025-09-09T00:34:51,758 include 2025-09-09T00:34:51,759 /usr/include/python3.13 2025-09-09T00:34:51,759 /usr/include/c++/14 2025-09-09T00:34:51,759 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:51,759 /usr/include/c++/14/backward 2025-09-09T00:34:51,759 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:51,759 /usr/local/include 2025-09-09T00:34:51,759 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:51,760 /usr/include 2025-09-09T00:34:51,760 End of search list. 2025-09-09T00:34:51,777 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:53,098 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:53,098 from ./src/charges/mmff94.cpp:20: 2025-09-09T00:34:53,098 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:53,099 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:53,099 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:53,099 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:53,099 from include/openbabel/plugin.h:23: 2025-09-09T00:34:53,099 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:53,099 131 | struct binary_function 2025-09-09T00:34:53,099 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:53,207 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:53,207 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:53,207 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:53,208 | ~~~~~~~^ 2025-09-09T00:34:53,208 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:53,208 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:53,208 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:53,208 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:53,310 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:53,311 from include/openbabel/mol.h:43, 2025-09-09T00:34:53,311 from ./src/charges/mmff94.cpp:21: 2025-09-09T00:34:53,311 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:53,311 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:53,311 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:53,311 | ^ 2025-09-09T00:34:53,311 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:53,311 37 | # define UNUSED(x) x 2025-09-09T00:34:53,311 | ^ 2025-09-09T00:34:53,900 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:53,900 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:53,900 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:53,900 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:53,900 | ^ 2025-09-09T00:34:53,900 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:53,900 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:53,901 | ^~~~~~~~ 2025-09-09T00:34:53,904 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:53,904 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:53,904 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:53,904 | ^ 2025-09-09T00:34:53,904 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:53,904 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:53,904 | ^~~~~~~~ 2025-09-09T00:34:53,918 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:53,918 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:53,918 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:53,918 | ^ 2025-09-09T00:34:53,919 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:53,919 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:53,919 | ^~~~~~~~ 2025-09-09T00:34:53,923 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:53,923 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:53,923 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:53,923 | ^ 2025-09-09T00:34:53,924 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:53,924 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:53,924 | ^~~~~~~~ 2025-09-09T00:34:54,083 In file included from include/openbabel/forcefield.h:33, 2025-09-09T00:34:54,083 from ./src/charges/mmff94.cpp:22: 2025-09-09T00:34:54,083 include/openbabel/grid.h: At global scope: 2025-09-09T00:34:54,083 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:34:54,083 55 | virtual void Init(OBMol &box); 2025-09-09T00:34:54,083 | ^~~~ 2025-09-09T00:34:54,084 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:34:54,084 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:34:54,084 | ^~~~ 2025-09-09T00:34:54,094 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:34:54,094 229 | virtual const std::string &GetValue() const 2025-09-09T00:34:54,094 | ^~~~~~~~ 2025-09-09T00:34:54,094 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:34:54,094 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:34:54,095 76 | double GetValue (vector3 pos) const; 2025-09-09T00:34:54,095 | ^~~~~~~~ 2025-09-09T00:34:54,148 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:34:54,148 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,148 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,148 | ^ 2025-09-09T00:34:54,148 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,149 37 | # define UNUSED(x) x 2025-09-09T00:34:54,149 | ^ 2025-09-09T00:34:54,149 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:34:54,149 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,149 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,149 | ^ 2025-09-09T00:34:54,149 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,149 37 | # define UNUSED(x) x 2025-09-09T00:34:54,149 | ^ 2025-09-09T00:34:54,150 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:34:54,150 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,150 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,150 | ^ 2025-09-09T00:34:54,150 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,150 37 | # define UNUSED(x) x 2025-09-09T00:34:54,150 | ^ 2025-09-09T00:34:54,150 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:34:54,150 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,151 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,151 | ^ 2025-09-09T00:34:54,151 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,151 37 | # define UNUSED(x) x 2025-09-09T00:34:54,151 | ^ 2025-09-09T00:34:54,151 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:34:54,151 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,151 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,151 | ^ 2025-09-09T00:34:54,151 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,152 37 | # define UNUSED(x) x 2025-09-09T00:34:54,152 | ^ 2025-09-09T00:34:54,152 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:34:54,152 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,152 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,152 | ^ 2025-09-09T00:34:54,152 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,152 37 | # define UNUSED(x) x 2025-09-09T00:34:54,152 | ^ 2025-09-09T00:34:54,152 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:34:54,153 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,153 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,153 | ^ 2025-09-09T00:34:54,153 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,153 37 | # define UNUSED(x) x 2025-09-09T00:34:54,153 | ^ 2025-09-09T00:34:54,153 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:34:54,153 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:34:54,153 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:34:54,153 | ^ 2025-09-09T00:34:54,154 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:54,154 37 | # define UNUSED(x) x 2025-09-09T00:34:54,154 | ^ 2025-09-09T00:34:56,328 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/mmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:56,328 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/mmff94.o /tmp/cc8vJyut.s 2025-09-09T00:34:56,340 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:56,520 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:34:56,520 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:34:56,520 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/mmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/mmff94.' 2025-09-09T00:34:56,521 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/none.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/none.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:34:56,526 Using built-in specs. 2025-09-09T00:34:56,527 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:56,527 Target: arm-linux-gnueabihf 2025-09-09T00:34:56,527 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:34:56,527 Thread model: posix 2025-09-09T00:34:56,527 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:56,527 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:56,527 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/none.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:34:56,527 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/none.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase none.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccgQ79Uj.s 2025-09-09T00:34:56,540 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:56,540 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:34:56,540 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:56,540 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:56,540 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:56,540 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:56,541 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:56,541 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:56,541 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:56,541 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:56,541 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:56,541 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:56,541 #include "..." search starts here: 2025-09-09T00:34:56,541 #include <...> search starts here: 2025-09-09T00:34:56,542 /usr/include/eigen3 2025-09-09T00:34:56,542 include 2025-09-09T00:34:56,542 /usr/include/python3.13 2025-09-09T00:34:56,542 /usr/include/c++/14 2025-09-09T00:34:56,542 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:56,542 /usr/include/c++/14/backward 2025-09-09T00:34:56,542 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:56,542 /usr/local/include 2025-09-09T00:34:56,542 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:56,543 /usr/include 2025-09-09T00:34:56,543 End of search list. 2025-09-09T00:34:56,560 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:57,858 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:57,859 from ./src/charges/none.cpp:21: 2025-09-09T00:34:57,859 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:57,859 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:57,859 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:57,860 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:57,860 from include/openbabel/plugin.h:23: 2025-09-09T00:34:57,860 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:57,860 131 | struct binary_function 2025-09-09T00:34:57,860 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:57,970 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:57,970 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:57,970 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:57,970 | ~~~~~~~^ 2025-09-09T00:34:57,970 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:57,970 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:57,970 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:57,970 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:58,069 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:58,070 from include/openbabel/mol.h:43, 2025-09-09T00:34:58,070 from ./src/charges/none.cpp:22: 2025-09-09T00:34:58,070 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:58,070 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:58,070 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:58,070 | ^ 2025-09-09T00:34:58,070 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:58,070 37 | # define UNUSED(x) x 2025-09-09T00:34:58,070 | ^ 2025-09-09T00:34:58,663 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:58,664 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:58,664 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:58,664 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:58,664 | ^ 2025-09-09T00:34:58,664 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:58,664 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:58,664 | ^~~~~~~~ 2025-09-09T00:34:58,668 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:58,668 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:58,669 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:58,669 | ^ 2025-09-09T00:34:58,669 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:58,669 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:58,669 | ^~~~~~~~ 2025-09-09T00:34:58,684 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:58,684 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:58,684 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:58,684 | ^ 2025-09-09T00:34:58,684 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:58,684 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:58,685 | ^~~~~~~~ 2025-09-09T00:34:58,689 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:58,690 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:58,690 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:58,690 | ^ 2025-09-09T00:34:58,690 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:58,690 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:58,690 | ^~~~~~~~ 2025-09-09T00:35:00,558 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/none.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:35:00,558 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/none.o /tmp/ccgQ79Uj.s 2025-09-09T00:35:00,563 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:35:00,679 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:35:00,679 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:35:00,679 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/none.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/none.' 2025-09-09T00:35:00,681 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/qeq.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/qeq.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:35:00,684 Using built-in specs. 2025-09-09T00:35:00,685 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:35:00,685 Target: arm-linux-gnueabihf 2025-09-09T00:35:00,685 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:35:00,686 Thread model: posix 2025-09-09T00:35:00,686 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:35:00,686 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:35:00,686 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/qeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:35:00,686 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/qeq.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase qeq.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccpwmFdL.s 2025-09-09T00:35:00,696 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:35:00,697 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:35:00,697 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:35:00,697 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:35:00,697 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:35:00,697 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:35:00,698 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:35:00,698 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:35:00,698 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:35:00,698 ignoring duplicate directory "/usr/include/" 2025-09-09T00:35:00,698 as it is a non-system directory that duplicates a system directory 2025-09-09T00:35:00,698 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:35:00,698 #include "..." search starts here: 2025-09-09T00:35:00,698 #include <...> search starts here: 2025-09-09T00:35:00,699 /usr/include/eigen3 2025-09-09T00:35:00,699 include 2025-09-09T00:35:00,699 /usr/include/python3.13 2025-09-09T00:35:00,699 /usr/include/c++/14 2025-09-09T00:35:00,699 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:00,699 /usr/include/c++/14/backward 2025-09-09T00:35:00,699 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:00,699 /usr/local/include 2025-09-09T00:35:00,699 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:00,700 /usr/include 2025-09-09T00:35:00,700 End of search list. 2025-09-09T00:35:00,714 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:35:02,366 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:35:02,366 from include/charges/qeq.h:22, 2025-09-09T00:35:02,366 from ./src/charges/qeq.cpp:19: 2025-09-09T00:35:02,367 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:35:02,367 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:35:02,367 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:02,367 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:35:02,367 from include/openbabel/plugin.h:23: 2025-09-09T00:35:02,368 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:35:02,368 131 | struct binary_function 2025-09-09T00:35:02,368 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:02,473 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:35:02,473 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:35:02,473 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:35:02,474 | ~~~~~~~^ 2025-09-09T00:35:02,474 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:35:02,474 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:35:02,474 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:35:02,474 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:35:02,575 In file included from include/openbabel/atom.h:33, 2025-09-09T00:35:02,575 from include/openbabel/mol.h:43, 2025-09-09T00:35:02,575 from include/charges/qeq.h:23: 2025-09-09T00:35:02,575 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:35:02,575 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:35:02,576 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:35:02,576 | ^ 2025-09-09T00:35:02,576 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:02,576 37 | # define UNUSED(x) x 2025-09-09T00:35:02,576 | ^ 2025-09-09T00:35:03,163 In file included from include/openbabel/mol.h:52: 2025-09-09T00:35:03,163 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:03,163 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:03,163 862 | {return new OBVibrationData(*this);} 2025-09-09T00:35:03,163 | ^ 2025-09-09T00:35:03,163 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:35:03,164 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:35:03,164 | ^~~~~~~~ 2025-09-09T00:35:03,167 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:03,167 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:03,167 907 | {return new OBDOSData(*this);} 2025-09-09T00:35:03,167 | ^ 2025-09-09T00:35:03,167 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:35:03,167 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:35:03,167 | ^~~~~~~~ 2025-09-09T00:35:03,182 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:03,182 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:03,183 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:35:03,183 | ^ 2025-09-09T00:35:03,183 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:35:03,183 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:35:03,183 | ^~~~~~~~ 2025-09-09T00:35:03,187 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:03,187 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:03,187 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:35:03,187 | ^ 2025-09-09T00:35:03,188 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:35:03,188 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:35:03,188 | ^~~~~~~~ 2025-09-09T00:35:05,113 ./src/charges/qeq.cpp: In member function ‘Eigen::Vector3d OpenBabel::QEqCharges::GetParameters(unsigned int, int)’: 2025-09-09T00:35:05,114 ./src/charges/qeq.cpp:148:58: warning: unused parameter ‘Q’ [-Wunused-parameter] 2025-09-09T00:35:05,114 148 | Vector3d QEqCharges::GetParameters(unsigned int Z, int Q) 2025-09-09T00:35:05,114 | ~~~~^ 2025-09-09T00:35:50,402 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/qeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:35:50,403 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/qeq.o /tmp/ccpwmFdL.s 2025-09-09T00:35:50,410 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:35:54,898 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:35:54,900 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:35:54,900 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/qeq.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/qeq.' 2025-09-09T00:35:54,917 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/charges/qtpie.cpp -o build/temp.linux-armv7l-cpython-313/src/charges/qtpie.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:35:54,922 Using built-in specs. 2025-09-09T00:35:54,923 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:35:54,924 Target: arm-linux-gnueabihf 2025-09-09T00:35:54,924 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:35:54,924 Thread model: posix 2025-09-09T00:35:54,924 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:35:54,924 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:35:54,924 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/qtpie.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:35:54,925 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/charges/qtpie.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/charges/ -dumpbase qtpie.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccjiCBQQ.s 2025-09-09T00:35:54,938 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:35:54,939 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:35:54,939 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:35:54,939 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:35:54,941 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:35:54,941 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:35:54,941 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:35:54,941 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:35:54,941 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:35:54,942 ignoring duplicate directory "/usr/include/" 2025-09-09T00:35:54,942 as it is a non-system directory that duplicates a system directory 2025-09-09T00:35:54,942 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:35:54,942 #include "..." search starts here: 2025-09-09T00:35:54,942 #include <...> search starts here: 2025-09-09T00:35:54,943 /usr/include/eigen3 2025-09-09T00:35:54,943 include 2025-09-09T00:35:54,943 /usr/include/python3.13 2025-09-09T00:35:54,943 /usr/include/c++/14 2025-09-09T00:35:54,943 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:54,943 /usr/include/c++/14/backward 2025-09-09T00:35:54,943 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:54,944 /usr/local/include 2025-09-09T00:35:54,944 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:54,944 /usr/include 2025-09-09T00:35:54,944 End of search list. 2025-09-09T00:35:54,960 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:35:56,609 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:35:56,609 from include/charges/qtpie.h:22, 2025-09-09T00:35:56,609 from ./src/charges/qtpie.cpp:19: 2025-09-09T00:35:56,609 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:35:56,609 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:35:56,609 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:56,610 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:35:56,610 from include/openbabel/plugin.h:23: 2025-09-09T00:35:56,610 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:35:56,610 131 | struct binary_function 2025-09-09T00:35:56,610 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:56,716 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:35:56,716 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:35:56,716 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:35:56,716 | ~~~~~~~^ 2025-09-09T00:35:56,717 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:35:56,717 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:35:56,717 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:35:56,717 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:35:56,817 In file included from include/openbabel/atom.h:33, 2025-09-09T00:35:56,817 from include/openbabel/mol.h:43, 2025-09-09T00:35:56,817 from include/charges/qtpie.h:23: 2025-09-09T00:35:56,817 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:35:56,818 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:35:56,818 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:35:56,818 | ^ 2025-09-09T00:35:56,818 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:56,818 37 | # define UNUSED(x) x 2025-09-09T00:35:56,818 | ^ 2025-09-09T00:35:57,407 In file included from include/openbabel/mol.h:52: 2025-09-09T00:35:57,407 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,407 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,408 862 | {return new OBVibrationData(*this);} 2025-09-09T00:35:57,408 | ^ 2025-09-09T00:35:57,408 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:35:57,408 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:35:57,408 | ^~~~~~~~ 2025-09-09T00:35:57,411 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,411 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,411 907 | {return new OBDOSData(*this);} 2025-09-09T00:35:57,411 | ^ 2025-09-09T00:35:57,412 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:35:57,412 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:35:57,412 | ^~~~~~~~ 2025-09-09T00:35:57,426 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,426 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,426 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:35:57,426 | ^ 2025-09-09T00:35:57,426 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:35:57,426 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:35:57,426 | ^~~~~~~~ 2025-09-09T00:35:57,430 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,431 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,431 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:35:57,431 | ^ 2025-09-09T00:35:57,431 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:35:57,431 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:35:57,431 | ^~~~~~~~ 2025-09-09T00:35:59,355 ./src/charges/qtpie.cpp: In member function ‘Eigen::Vector3d OpenBabel::QTPIECharges::GetParameters(unsigned int, int)’: 2025-09-09T00:35:59,356 ./src/charges/qtpie.cpp:145:60: warning: unused parameter ‘Q’ [-Wunused-parameter] 2025-09-09T00:35:59,356 145 | Vector3d QTPIECharges::GetParameters(unsigned int Z, int Q) 2025-09-09T00:35:59,356 | ~~~~^ 2025-09-09T00:36:45,041 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/qtpie.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/' 2025-09-09T00:36:45,041 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/charges/qtpie.o /tmp/ccjiCBQQ.s 2025-09-09T00:36:45,046 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:49,668 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:36:49,668 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:36:49,668 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/charges/qtpie.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/charges/qtpie.' 2025-09-09T00:36:49,687 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/chiral.cpp -o build/temp.linux-armv7l-cpython-313/src/chiral.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:36:49,692 Using built-in specs. 2025-09-09T00:36:49,693 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:49,693 Target: arm-linux-gnueabihf 2025-09-09T00:36:49,693 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:36:49,694 Thread model: posix 2025-09-09T00:36:49,694 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:49,694 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:49,694 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chiral.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:36:49,694 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/chiral.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase chiral.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccg01Hv1.s 2025-09-09T00:36:49,707 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:49,708 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:36:49,708 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:49,708 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:49,708 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:49,708 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:49,709 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:49,709 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:49,709 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:49,709 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:49,709 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:49,710 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:49,710 #include "..." search starts here: 2025-09-09T00:36:49,710 #include <...> search starts here: 2025-09-09T00:36:49,710 /usr/include/eigen3 2025-09-09T00:36:49,710 include 2025-09-09T00:36:49,710 /usr/include/python3.13 2025-09-09T00:36:49,710 /usr/include/c++/14 2025-09-09T00:36:49,711 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:49,711 /usr/include/c++/14/backward 2025-09-09T00:36:49,711 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:49,711 /usr/local/include 2025-09-09T00:36:49,711 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:49,711 /usr/include 2025-09-09T00:36:49,711 End of search list. 2025-09-09T00:36:49,730 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:51,234 In file included from include/openbabel/atom.h:33, 2025-09-09T00:36:51,234 from include/openbabel/mol.h:43, 2025-09-09T00:36:51,234 from ./src/chiral.cpp:23: 2025-09-09T00:36:51,234 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:51,234 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:51,234 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:51,235 | ^ 2025-09-09T00:36:51,235 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:51,235 37 | # define UNUSED(x) x 2025-09-09T00:36:51,235 | ^ 2025-09-09T00:36:51,810 In file included from include/openbabel/mol.h:52: 2025-09-09T00:36:51,810 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,810 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,810 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:51,811 | ^ 2025-09-09T00:36:51,811 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:51,811 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:51,811 | ^~~~~~~~ 2025-09-09T00:36:51,815 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,815 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,815 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:51,815 | ^ 2025-09-09T00:36:51,816 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:51,816 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:51,816 | ^~~~~~~~ 2025-09-09T00:36:51,830 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,830 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,831 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:51,831 | ^ 2025-09-09T00:36:51,831 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:51,831 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:51,831 | ^~~~~~~~ 2025-09-09T00:36:51,836 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,836 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,836 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:51,836 | ^ 2025-09-09T00:36:51,837 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:51,837 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:51,837 | ^~~~~~~~ 2025-09-09T00:36:55,370 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chiral.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:36:55,372 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/chiral.o /tmp/ccg01Hv1.s 2025-09-09T00:36:55,380 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:55,657 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:36:55,658 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:36:55,658 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/chiral.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/chiral.' 2025-09-09T00:36:55,660 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/conformersearch.cpp -o build/temp.linux-armv7l-cpython-313/src/conformersearch.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:36:55,664 Using built-in specs. 2025-09-09T00:36:55,665 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:55,665 Target: arm-linux-gnueabihf 2025-09-09T00:36:55,666 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:36:55,666 Thread model: posix 2025-09-09T00:36:55,666 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:55,666 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:55,667 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/conformersearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:36:55,668 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/conformersearch.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase conformersearch.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccHPaXr1.s 2025-09-09T00:36:55,682 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:55,682 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:36:55,683 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:55,683 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:55,685 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:55,686 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:55,686 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:55,686 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:55,687 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:55,687 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:55,687 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:55,687 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:55,688 #include "..." search starts here: 2025-09-09T00:36:55,688 #include <...> search starts here: 2025-09-09T00:36:55,688 /usr/include/eigen3 2025-09-09T00:36:55,688 include 2025-09-09T00:36:55,689 /usr/include/python3.13 2025-09-09T00:36:55,689 /usr/include/c++/14 2025-09-09T00:36:55,689 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:55,689 /usr/include/c++/14/backward 2025-09-09T00:36:55,689 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:55,689 /usr/local/include 2025-09-09T00:36:55,690 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:55,690 /usr/include 2025-09-09T00:36:55,690 End of search list. 2025-09-09T00:36:55,706 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:57,512 In file included from include/openbabel/atom.h:33, 2025-09-09T00:36:57,513 from include/openbabel/mol.h:43, 2025-09-09T00:36:57,513 from include/openbabel/conformersearch.h:24, 2025-09-09T00:36:57,513 from ./src/conformersearch.cpp:20: 2025-09-09T00:36:57,513 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:57,513 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:57,513 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:57,513 | ^ 2025-09-09T00:36:57,513 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:57,513 37 | # define UNUSED(x) x 2025-09-09T00:36:57,513 | ^ 2025-09-09T00:36:58,125 In file included from include/openbabel/mol.h:52: 2025-09-09T00:36:58,125 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:58,126 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:58,126 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:58,126 | ^ 2025-09-09T00:36:58,126 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:58,126 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:58,126 | ^~~~~~~~ 2025-09-09T00:36:58,130 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:58,130 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:58,130 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:58,131 | ^ 2025-09-09T00:36:58,131 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:58,131 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:58,131 | ^~~~~~~~ 2025-09-09T00:36:58,146 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:58,146 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:58,146 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:58,146 | ^ 2025-09-09T00:36:58,146 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:58,146 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:58,146 | ^~~~~~~~ 2025-09-09T00:36:58,151 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:58,152 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:58,152 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:58,152 | ^ 2025-09-09T00:36:58,152 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:58,152 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:58,152 | ^~~~~~~~ 2025-09-09T00:36:58,317 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:36:58,317 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:36:58,317 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:36:58,317 | ^ 2025-09-09T00:36:58,317 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:58,317 37 | # define UNUSED(x) x 2025-09-09T00:36:58,317 | ^ 2025-09-09T00:36:58,318 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:36:58,318 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:36:58,318 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:36:58,318 | ^ 2025-09-09T00:36:58,318 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:58,319 37 | # define UNUSED(x) x 2025-09-09T00:36:58,319 | ^ 2025-09-09T00:36:59,794 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:36:59,794 from ./src/conformersearch.cpp:22: 2025-09-09T00:36:59,794 include/openbabel/plugin.h: At global scope: 2025-09-09T00:36:59,794 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:36:59,794 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:36:59,795 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:59,795 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:36:59,795 from /usr/include/c++/14/vector:68, 2025-09-09T00:36:59,796 from include/openbabel/mol.h:35: 2025-09-09T00:36:59,796 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:36:59,796 131 | struct binary_function 2025-09-09T00:36:59,796 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:59,831 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:36:59,831 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:36:59,831 55 | virtual void Init(OBMol &box); 2025-09-09T00:36:59,831 | ^~~~ 2025-09-09T00:36:59,832 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:36:59,832 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:36:59,832 | ^~~~ 2025-09-09T00:36:59,843 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:36:59,843 229 | virtual const std::string &GetValue() const 2025-09-09T00:36:59,843 | ^~~~~~~~ 2025-09-09T00:36:59,844 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:36:59,844 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:36:59,844 76 | double GetValue (vector3 pos) const; 2025-09-09T00:36:59,844 | ^~~~~~~~ 2025-09-09T00:36:59,898 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:36:59,899 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,899 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,899 | ^ 2025-09-09T00:36:59,899 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,899 37 | # define UNUSED(x) x 2025-09-09T00:36:59,899 | ^ 2025-09-09T00:36:59,900 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:36:59,900 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,900 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,900 | ^ 2025-09-09T00:36:59,900 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,900 37 | # define UNUSED(x) x 2025-09-09T00:36:59,900 | ^ 2025-09-09T00:36:59,901 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:36:59,901 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,901 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,901 | ^ 2025-09-09T00:36:59,901 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,901 37 | # define UNUSED(x) x 2025-09-09T00:36:59,901 | ^ 2025-09-09T00:36:59,901 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:36:59,902 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,902 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,902 | ^ 2025-09-09T00:36:59,902 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,902 37 | # define UNUSED(x) x 2025-09-09T00:36:59,902 | ^ 2025-09-09T00:36:59,902 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:36:59,903 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,903 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,903 | ^ 2025-09-09T00:36:59,903 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,903 37 | # define UNUSED(x) x 2025-09-09T00:36:59,903 | ^ 2025-09-09T00:36:59,903 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:36:59,903 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,904 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,904 | ^ 2025-09-09T00:36:59,904 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,904 37 | # define UNUSED(x) x 2025-09-09T00:36:59,904 | ^ 2025-09-09T00:36:59,904 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:36:59,904 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,904 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,905 | ^ 2025-09-09T00:36:59,905 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,905 37 | # define UNUSED(x) x 2025-09-09T00:36:59,905 | ^ 2025-09-09T00:36:59,905 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:36:59,905 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:36:59,905 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:36:59,905 | ^ 2025-09-09T00:36:59,906 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:59,906 37 | # define UNUSED(x) x 2025-09-09T00:36:59,906 | ^ 2025-09-09T00:36:59,917 ./src/conformersearch.cpp: In member function ‘virtual bool OpenBabel::OBStericConformerFilter::IsGood(const OpenBabel::OBMol&, const OpenBabel::RotorKey&, double*)’: 2025-09-09T00:36:59,917 ./src/conformersearch.cpp:48:74: warning: unused parameter ‘key’ [-Wunused-parameter] 2025-09-09T00:36:59,917 48 | bool OBStericConformerFilter::IsGood(const OBMol &mol, const RotorKey &key, double *conformer) 2025-09-09T00:36:59,917 | ~~~~~~~~~~~~~~~~^~~ 2025-09-09T00:36:59,924 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2025-09-09T00:36:59,924 ./src/conformersearch.cpp:97:55: warning: unused parameter ‘keys’ [-Wunused-parameter] 2025-09-09T00:36:59,924 97 | const RotorKeys &keys, const std::vector &conformers) 2025-09-09T00:36:59,924 | ~~~~~~~~~~~~~~~~~^~~~ 2025-09-09T00:36:59,941 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2025-09-09T00:36:59,941 ./src/conformersearch.cpp:240:12: warning: unused variable ‘score’ [-Wunused-variable] 2025-09-09T00:36:59,941 240 | double score = ff->Energy(false); // no gradients 2025-09-09T00:36:59,941 | ^~~~~ 2025-09-09T00:36:59,942 ./src/conformersearch.cpp:221:65: warning: unused parameter ‘keys’ [-Wunused-parameter] 2025-09-09T00:36:59,942 221 | const RotorKeys &keys, const std::vector &conformers) 2025-09-09T00:36:59,942 | ~~~~~~~~~~~~~~~~~^~~~ 2025-09-09T00:36:59,950 ./src/conformersearch.cpp: In member function ‘bool OpenBabel::OBConformerSearch::Setup(const OpenBabel::OBMol&, int, int, int, int)’: 2025-09-09T00:36:59,951 ./src/conformersearch.cpp:337:23: warning: variable ‘end_it’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:36:59,951 337 | OBRotorIterator end_it = m_rotorList.EndRotors(); 2025-09-09T00:36:59,951 | ^~~~~~ 2025-09-09T00:37:00,008 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::local_opt()’: 2025-09-09T00:37:00,009 ./src/conformersearch.cpp:775:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:00,009 775 | for (i = 1; i <= m_rotorList.Size(); ++i, rotor = m_rotorList.NextRotor(ri)) 2025-09-09T00:37:00,009 | ~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:00,014 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::reproduce(OpenBabel::RotorKey&, OpenBabel::RotorKey&)’: 2025-09-09T00:37:00,014 ./src/conformersearch.cpp:836:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:00,014 836 | if (iniche > -1) 2025-09-09T00:37:00,014 | ~~~~~~~^~~~ 2025-09-09T00:37:00,027 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::share_fitness()’: 2025-09-09T00:37:00,027 ./src/conformersearch.cpp:991:37: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-09T00:37:00,028 991 | if ((dynamic_niches.size () < nb_niches) && (dynamic_niches.size () %2)) 2025-09-09T00:37:00,028 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:37:00,029 ./src/conformersearch.cpp:1006:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:37:00,029 1006 | if (dist < min_dist ) 2025-09-09T00:37:00,029 | ~~~~~^~~~~~~~~~ 2025-09-09T00:37:00,029 ./src/conformersearch.cpp:1019:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:00,030 1019 | if (imax == -1) 2025-09-09T00:37:00,030 | ~~~~~^~~~~ 2025-09-09T00:37:00,031 ./src/conformersearch.cpp:1035:40: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-09T00:37:00,031 1035 | if (dynamic_niches.size () < nb_niches) 2025-09-09T00:37:00,031 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:37:00,034 ./src/conformersearch.cpp:962:10: warning: unused variable ‘flag_niched’ [-Wunused-variable] 2025-09-09T00:37:00,034 962 | bool flag_niched = false; 2025-09-09T00:37:00,034 | ^~~~~~~~~~~ 2025-09-09T00:37:00,042 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::sharing_generation()’: 2025-09-09T00:37:00,042 ./src/conformersearch.cpp:1124:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:37:00,042 1124 | while (ninsert < ((half_pop * 2) / 3)) 2025-09-09T00:37:00,042 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:00,043 ./src/conformersearch.cpp:1133:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:37:00,043 1133 | if (iround < imax) 2025-09-09T00:37:00,043 | ~~~~~~~^~~~~~ 2025-09-09T00:37:00,044 ./src/conformersearch.cpp:1141:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:37:00,044 1141 | if (ninsert >= half_pop) 2025-09-09T00:37:00,044 | ~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:37:00,045 ./src/conformersearch.cpp:1166:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:37:00,045 1166 | while (ninsert < half_pop) 2025-09-09T00:37:00,045 | ~~~~~~~~^~~~~~~~~~ 2025-09-09T00:37:00,048 ./src/conformersearch.cpp:1090:23: warning: unused variable ‘lowest’ [-Wunused-variable] 2025-09-09T00:37:00,048 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2025-09-09T00:37:00,048 | ^~~~~~ 2025-09-09T00:37:00,048 ./src/conformersearch.cpp:1090:37: warning: unused variable ‘highest’ [-Wunused-variable] 2025-09-09T00:37:00,048 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2025-09-09T00:37:00,048 | ^~~~~~~ 2025-09-09T00:37:03,761 In file included from /usr/include/c++/14/algorithm:61, 2025-09-09T00:37:03,762 from include/openbabel/ring.h:24, 2025-09-09T00:37:03,762 from include/openbabel/mol.h:51: 2025-09-09T00:37:03,762 /usr/include/c++/14/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]’: 2025-09-09T00:37:03,762 /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:03,762 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, 2025-09-09T00:37:03,762 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:03,825 /usr/include/c++/14/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]’: 2025-09-09T00:37:03,825 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:03,825 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:37:03,825 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:37:03,826 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:03,882 /usr/include/c++/14/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]’: 2025-09-09T00:37:03,882 /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:03,882 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, 2025-09-09T00:37:03,882 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:03,944 /usr/include/c++/14/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]’: 2025-09-09T00:37:03,944 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:03,944 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:37:03,944 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:37:03,945 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:04,099 In file included from /usr/include/c++/14/bits/stl_algo.h:61: 2025-09-09T00:37:04,099 /usr/include/c++/14/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]’: 2025-09-09T00:37:04,099 /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:04,099 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:37:04,100 | ^~~~~~~~~~~~~ 2025-09-09T00:37:04,361 /usr/include/c++/14/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]’: 2025-09-09T00:37:04,361 /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,188 /usr/include/c++/14/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]’: 2025-09-09T00:37:07,189 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,189 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:37:07,189 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,189 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,192 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,192 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:37:07,192 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,461 /usr/include/c++/14/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]’: 2025-09-09T00:37:07,462 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,462 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:37:07,462 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,462 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,465 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,465 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:37:07,465 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,825 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:07,825 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:07,825 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2025-09-09T00:37:07,825 /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,825 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:37:07,825 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,825 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:37:07,825 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,825 1907 | __comp); 2025-09-09T00:37:07,825 | ~~~~~~~ 2025-09-09T00:37:07,826 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:07,826 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++/14/bits/stl_algo.h:1908:31, 2025-09-09T00:37:07,826 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:07,826 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2025-09-09T00:37:07,826 /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,827 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:37:07,827 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,827 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,827 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:37:07,827 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,828 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:07,828 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:07,828 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2025-09-09T00:37:07,828 /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,828 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:37:07,828 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,828 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:37:07,828 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,828 1907 | __comp); 2025-09-09T00:37:07,828 | ~~~~~~~ 2025-09-09T00:37:07,829 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:07,829 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++/14/bits/stl_algo.h:1908:31, 2025-09-09T00:37:07,829 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:07,829 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2025-09-09T00:37:07,829 /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,829 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:37:07,830 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:07,830 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:07,830 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:37:07,830 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,331 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::MakeSelection()’: 2025-09-09T00:37:09,331 ./src/conformersearch.cpp:535:31: warning: ‘highest’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:09,331 535 | double sum = 0.0, lowest, highest; 2025-09-09T00:37:09,331 | ^~~~~~~ 2025-09-09T00:37:09,343 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:09,343 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:09,344 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2025-09-09T00:37:09,344 /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:09,344 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:37:09,344 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,344 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:37:09,344 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,344 1907 | __comp); 2025-09-09T00:37:09,344 | ~~~~~~~ 2025-09-09T00:37:09,345 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:09,345 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++/14/bits/stl_algo.h:1908:31, 2025-09-09T00:37:09,345 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerHighScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:09,345 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2025-09-09T00:37:09,345 /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:09,345 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:37:09,345 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,346 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:09,346 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:37:09,346 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,346 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:09,347 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:09,347 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2025-09-09T00:37:09,347 /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:09,347 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:37:09,347 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,347 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:37:09,347 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,347 1907 | __comp); 2025-09-09T00:37:09,347 | ~~~~~~~ 2025-09-09T00:37:09,348 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:37:09,348 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++/14/bits/stl_algo.h:1908:31, 2025-09-09T00:37:09,348 inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = OpenBabel::CompareConformerLowScore]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:09,348 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2025-09-09T00:37:09,348 /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:09,348 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:37:09,348 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:09,349 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:09,349 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:37:09,349 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:10,154 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:37:10,155 from include/openbabel/mol.h:37: 2025-09-09T00:37:10,155 /usr/include/c++/14/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> >]’: 2025-09-09T00:37:10,155 /usr/include/c++/14/bits/stl_tree.h:2208:5: 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 2025-09-09T00:37:10,155 2208 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:37:10,155 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:12,594 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/conformersearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:37:12,595 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/conformersearch.o /tmp/ccHPaXr1.s 2025-09-09T00:37:12,600 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:13,871 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:37:13,871 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:37:13,872 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/conformersearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/conformersearch.' 2025-09-09T00:37:13,877 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/confsearch.cpp -o build/temp.linux-armv7l-cpython-313/src/confsearch.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:37:13,881 Using built-in specs. 2025-09-09T00:37:13,882 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:13,882 Target: arm-linux-gnueabihf 2025-09-09T00:37:13,882 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:37:13,882 Thread model: posix 2025-09-09T00:37:13,883 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:13,883 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:13,883 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/confsearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:37:13,885 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/confsearch.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase confsearch.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cceXIlSd.s 2025-09-09T00:37:13,897 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:13,898 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:37:13,898 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:13,898 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:13,899 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:13,900 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:13,900 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:13,900 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:13,900 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:13,901 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:13,901 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:13,901 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:13,901 #include "..." search starts here: 2025-09-09T00:37:13,902 #include <...> search starts here: 2025-09-09T00:37:13,902 /usr/include/eigen3 2025-09-09T00:37:13,902 include 2025-09-09T00:37:13,902 /usr/include/python3.13 2025-09-09T00:37:13,902 /usr/include/c++/14 2025-09-09T00:37:13,903 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:13,903 /usr/include/c++/14/backward 2025-09-09T00:37:13,903 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:13,903 /usr/local/include 2025-09-09T00:37:13,903 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:13,904 /usr/include 2025-09-09T00:37:13,904 End of search list. 2025-09-09T00:37:13,922 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:15,802 In file included from include/openbabel/forcefield.h:30, 2025-09-09T00:37:15,802 from ./src/confsearch.cpp:23: 2025-09-09T00:37:15,802 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:15,802 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:15,802 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:15,802 | ^ 2025-09-09T00:37:15,802 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:15,802 37 | # define UNUSED(x) x 2025-09-09T00:37:15,803 | ^ 2025-09-09T00:37:16,438 In file included from include/openbabel/mol.h:52, 2025-09-09T00:37:16,438 from include/openbabel/forcefield.h:31: 2025-09-09T00:37:16,438 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:16,438 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:16,438 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:16,438 | ^ 2025-09-09T00:37:16,438 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:16,439 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:16,439 | ^~~~~~~~ 2025-09-09T00:37:16,443 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:16,443 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:16,443 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:16,443 | ^ 2025-09-09T00:37:16,443 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:16,443 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:16,443 | ^~~~~~~~ 2025-09-09T00:37:16,458 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:16,458 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:16,458 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:16,459 | ^ 2025-09-09T00:37:16,459 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:16,459 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:16,459 | ^~~~~~~~ 2025-09-09T00:37:16,464 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:16,465 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:16,465 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:16,465 | ^ 2025-09-09T00:37:16,465 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:16,465 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:16,465 | ^~~~~~~~ 2025-09-09T00:37:16,605 In file included from include/openbabel/forcefield.h:32: 2025-09-09T00:37:16,605 include/openbabel/plugin.h: At global scope: 2025-09-09T00:37:16,605 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:37:16,605 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:37:16,605 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:16,606 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:37:16,606 from /usr/include/c++/14/vector:68, 2025-09-09T00:37:16,606 from include/openbabel/forcefield.h:23: 2025-09-09T00:37:16,606 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:37:16,606 131 | struct binary_function 2025-09-09T00:37:16,606 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:16,640 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:37:16,640 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:37:16,640 55 | virtual void Init(OBMol &box); 2025-09-09T00:37:16,640 | ^~~~ 2025-09-09T00:37:16,641 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:37:16,641 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:37:16,641 | ^~~~ 2025-09-09T00:37:16,652 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:37:16,652 229 | virtual const std::string &GetValue() const 2025-09-09T00:37:16,652 | ^~~~~~~~ 2025-09-09T00:37:16,652 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:37:16,653 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:37:16,653 76 | double GetValue (vector3 pos) const; 2025-09-09T00:37:16,653 | ^~~~~~~~ 2025-09-09T00:37:16,707 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:37:16,707 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,707 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,707 | ^ 2025-09-09T00:37:16,707 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,707 37 | # define UNUSED(x) x 2025-09-09T00:37:16,708 | ^ 2025-09-09T00:37:16,708 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:37:16,708 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,708 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,708 | ^ 2025-09-09T00:37:16,708 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,708 37 | # define UNUSED(x) x 2025-09-09T00:37:16,709 | ^ 2025-09-09T00:37:16,709 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:37:16,709 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,709 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,709 | ^ 2025-09-09T00:37:16,709 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,709 37 | # define UNUSED(x) x 2025-09-09T00:37:16,710 | ^ 2025-09-09T00:37:16,710 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:37:16,710 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,710 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,710 | ^ 2025-09-09T00:37:16,710 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,710 37 | # define UNUSED(x) x 2025-09-09T00:37:16,710 | ^ 2025-09-09T00:37:16,711 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:37:16,711 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,711 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,711 | ^ 2025-09-09T00:37:16,711 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,711 37 | # define UNUSED(x) x 2025-09-09T00:37:16,711 | ^ 2025-09-09T00:37:16,712 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:37:16,712 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,712 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,712 | ^ 2025-09-09T00:37:16,712 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,712 37 | # define UNUSED(x) x 2025-09-09T00:37:16,712 | ^ 2025-09-09T00:37:16,713 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:37:16,713 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,713 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,713 | ^ 2025-09-09T00:37:16,713 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,713 37 | # define UNUSED(x) x 2025-09-09T00:37:16,713 | ^ 2025-09-09T00:37:16,714 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:37:16,714 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:16,714 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:16,714 | ^ 2025-09-09T00:37:16,714 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,714 37 | # define UNUSED(x) x 2025-09-09T00:37:16,714 | ^ 2025-09-09T00:37:16,748 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:37:16,749 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:37:16,749 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:37:16,749 | ^ 2025-09-09T00:37:16,749 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,749 37 | # define UNUSED(x) x 2025-09-09T00:37:16,749 | ^ 2025-09-09T00:37:16,750 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:37:16,750 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:37:16,750 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:37:16,750 | ^ 2025-09-09T00:37:16,750 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:16,751 37 | # define UNUSED(x) x 2025-09-09T00:37:16,751 | ^ 2025-09-09T00:37:18,546 ./src/confsearch.cpp: In member function ‘unsigned int OpenBabel::LFSR::GetNext()’: 2025-09-09T00:37:18,546 ./src/confsearch.cpp:86:47: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 2025-09-09T00:37:18,547 86 | _lfsr = (_lfsr >> 1) ^ (unsigned int)(0 - (_lfsr & 1u) & _poly); 2025-09-09T00:37:18,547 | ~~^~~~~~~~~~~~~~ 2025-09-09T00:37:18,557 ./src/confsearch.cpp: In constructor ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’: 2025-09-09T00:37:18,557 ./src/confsearch.cpp:125:20: warning: ‘OpenBabel::OBDiversePoses::cutoff’ will be initialized after [-Wreorder] 2025-09-09T00:37:18,557 125 | const double cutoff; 2025-09-09T00:37:18,557 | ^~~~~~ 2025-09-09T00:37:18,558 ./src/confsearch.cpp:119:12: warning: ‘bool OpenBabel::OBDiversePoses::_percise’ [-Wreorder] 2025-09-09T00:37:18,558 119 | bool _percise; 2025-09-09T00:37:18,558 | ^~~~~~~~ 2025-09-09T00:37:18,558 ./src/confsearch.cpp:139:3: warning: when initialized here [-Wreorder] 2025-09-09T00:37:18,558 139 | OBDiversePoses::OBDiversePoses(const OBMol &ref, double RMSD, bool percise): 2025-09-09T00:37:18,558 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:18,561 ./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] 2025-09-09T00:37:18,561 149 | vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less(), (cutoff + 0.1) )), vec.end()); 2025-09-09T00:37:18,561 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:18,561 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:37:18,562 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:37:18,562 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:37:18,562 | ^~~~~~~ 2025-09-09T00:37:18,570 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(double*, double, int)’: 2025-09-09T00:37:18,571 ./src/confsearch.cpp:166:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:18,571 166 | for (unsigned int a = 0; a < natoms; ++a) 2025-09-09T00:37:18,571 | ~~^~~~~~~~ 2025-09-09T00:37:18,601 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’: 2025-09-09T00:37:18,601 ./src/confsearch.cpp:205:14: warning: unused variable ‘min_rmsd’ [-Wunused-variable] 2025-09-09T00:37:18,601 205 | double min_rmsd = DBL_MAX; 2025-09-09T00:37:18,601 | ^~~~~~~~ 2025-09-09T00:37:18,605 ./src/confsearch.cpp:269:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:18,605 269 | for (int k = *c; k < levels.size(); ++k) { 2025-09-09T00:37:18,605 | ~~^~~~~~~~~~~~~~~ 2025-09-09T00:37:18,607 ./src/confsearch.cpp: In member function ‘std::vector OpenBabel::OBDiversePoses::GetHeavyAtomCoords(const std::vector&)’: 2025-09-09T00:37:18,608 ./src/confsearch.cpp:283:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:18,608 283 | for (unsigned int a = 0; a < natoms; ++a) 2025-09-09T00:37:18,608 | ~~^~~~~~~~ 2025-09-09T00:37:18,625 ./src/confsearch.cpp: In member function ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’: 2025-09-09T00:37:18,626 ./src/confsearch.cpp:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:18,626 426 | for (int i = 1; i < rl.Size() + 1; ++i, rotor = rl.NextRotor(ri)) { // foreach rotor 2025-09-09T00:37:18,626 | ~~^~~~~~~~~~~~~~~ 2025-09-09T00:37:18,636 ./src/confsearch.cpp:464:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:18,636 464 | for (int i = 0 ; i < rotor_sizes.size(); ++i) { 2025-09-09T00:37:18,637 | ~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:18,638 ./src/confsearch.cpp:479:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:37:18,638 479 | } while (combination != 1 && counter < nconfs); // The LFSR always terminates with a 1 2025-09-09T00:37:18,638 | ~~~~~~~~^~~~~~~~ 2025-09-09T00:37:18,641 ./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] 2025-09-09T00:37:18,642 489 | transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(plus(), energy_offset)); 2025-09-09T00:37:18,642 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:18,642 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:37:18,642 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:37:18,642 | ^~~~~~~ 2025-09-09T00:37:18,643 ./src/confsearch.cpp:402:9: warning: unused variable ‘origLogLevel’ [-Wunused-variable] 2025-09-09T00:37:18,644 402 | int origLogLevel = _loglvl; 2025-09-09T00:37:18,644 | ^~~~~~~~~~~~ 2025-09-09T00:37:23,826 In file included from /usr/include/c++/14/vector:62: 2025-09-09T00:37:23,826 /usr/include/c++/14/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 > >]’: 2025-09-09T00:37:23,826 /usr/include/c++/14/bits/stl_algobase.h:2171:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:23,826 2171 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, 2025-09-09T00:37:23,827 | ^~~~~~~~~~~ 2025-09-09T00:37:23,827 /usr/include/c++/14/bits/stl_algobase.h:2171:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:24,009 In file included from /usr/include/c++/14/algorithm:61, 2025-09-09T00:37:24,009 from include/openbabel/ring.h:24, 2025-09-09T00:37:24,009 from include/openbabel/mol.h:51: 2025-09-09T00:37:24,009 In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator >; _Predicate = binder2nd >]’, 2025-09-09T00:37:24,010 inlined from ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’ at ./src/confsearch.cpp:149:29: 2025-09-09T00:37:24,010 /usr/include/c++/14/bits/stl_algo.h:832:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:37:24,010 832 | return std::__remove_if(__first, __last, 2025-09-09T00:37:24,010 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:37:24,010 833 | __gnu_cxx::__ops::__pred_iter(__pred)); 2025-09-09T00:37:24,010 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:25,574 /usr/include/c++/14/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>&)>]’: 2025-09-09T00:37:25,574 /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:25,574 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, 2025-09-09T00:37:25,574 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:25,644 /usr/include/c++/14/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>&)>]’: 2025-09-09T00:37:25,645 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:25,645 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:37:25,645 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:37:25,645 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:25,734 In file included from /usr/include/c++/14/bits/stl_algo.h:61: 2025-09-09T00:37:25,734 /usr/include/c++/14/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>&)>]’: 2025-09-09T00:37:25,734 /usr/include/c++/14/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 2025-09-09T00:37:25,734 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:37:25,735 | ^~~~~~~~~~~~~ 2025-09-09T00:37:25,842 /usr/include/c++/14/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>&)>]’: 2025-09-09T00:37:25,842 /usr/include/c++/14/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 2025-09-09T00:37:25,842 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, 2025-09-09T00:37:25,842 | ^~~~~~~~~~~ 2025-09-09T00:37:25,843 /usr/include/c++/14/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 2025-09-09T00:37:25,985 /usr/include/c++/14/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>&)>]’: 2025-09-09T00:37:25,985 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:25,985 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:37:25,985 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:37:25,986 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:25,986 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>&)>]’, 2025-09-09T00:37:25,986 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++/14/bits/stl_algo.h:1868:25, 2025-09-09T00:37:25,987 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++/14/bits/stl_algo.h:1884:27: 2025-09-09T00:37:25,987 /usr/include/c++/14/bits/stl_algo.h:1593:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:25,987 1593 | std::__make_heap(__first, __middle, __comp); 2025-09-09T00:37:25,987 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:25,990 /usr/include/c++/14/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>&)>]’: 2025-09-09T00:37:25,990 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:25,990 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:37:25,990 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,369 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>&)>]’, 2025-09-09T00:37:26,369 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++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:26,369 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2025-09-09T00:37:26,369 /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:26,370 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:37:26,370 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,370 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:37:26,370 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,370 1907 | __comp); 2025-09-09T00:37:26,370 | ~~~~~~~ 2025-09-09T00:37:26,370 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>&)>]’, 2025-09-09T00:37:26,370 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++/14/bits/stl_algo.h:1908:31, 2025-09-09T00:37:26,370 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++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:37:26,371 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2025-09-09T00:37:26,371 /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:26,371 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:37:26,371 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,371 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double, int>*, std::vector, double, int> > >’ changed in GCC 7.1 2025-09-09T00:37:26,371 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:37:26,371 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:30,523 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/confsearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:37:30,523 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/confsearch.o /tmp/cceXIlSd.s 2025-09-09T00:37:30,529 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:31,621 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:37:31,621 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:37:31,621 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/confsearch.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/confsearch.' 2025-09-09T00:37:31,626 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/data.cpp -o build/temp.linux-armv7l-cpython-313/src/data.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:37:31,629 Using built-in specs. 2025-09-09T00:37:31,630 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:31,631 Target: arm-linux-gnueabihf 2025-09-09T00:37:31,631 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:37:31,631 Thread model: posix 2025-09-09T00:37:31,632 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:31,632 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:31,632 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/data.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:37:31,635 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/data.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase data.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccuShSUk.s 2025-09-09T00:37:31,647 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:31,647 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:37:31,648 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:31,648 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:31,649 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:31,649 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:31,649 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:31,649 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:31,650 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:31,650 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:31,650 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:31,650 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:31,650 #include "..." search starts here: 2025-09-09T00:37:31,651 #include <...> search starts here: 2025-09-09T00:37:31,651 /usr/include/eigen3 2025-09-09T00:37:31,651 include 2025-09-09T00:37:31,651 /usr/include/python3.13 2025-09-09T00:37:31,651 /usr/include/c++/14 2025-09-09T00:37:31,651 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:31,652 /usr/include/c++/14/backward 2025-09-09T00:37:31,652 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:31,652 /usr/local/include 2025-09-09T00:37:31,652 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:31,652 /usr/include 2025-09-09T00:37:31,652 End of search list. 2025-09-09T00:37:31,671 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:33,245 In file included from include/openbabel/atom.h:33, 2025-09-09T00:37:33,245 from include/openbabel/mol.h:43, 2025-09-09T00:37:33,245 from include/openbabel/data_utilities.h:25, 2025-09-09T00:37:33,245 from ./src/data.cpp:22: 2025-09-09T00:37:33,245 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:33,246 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:33,246 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:33,246 | ^ 2025-09-09T00:37:33,246 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:33,246 37 | # define UNUSED(x) x 2025-09-09T00:37:33,246 | ^ 2025-09-09T00:37:33,785 In file included from include/openbabel/mol.h:52: 2025-09-09T00:37:33,785 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:33,785 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:33,786 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:33,786 | ^ 2025-09-09T00:37:33,786 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:33,786 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:33,786 | ^~~~~~~~ 2025-09-09T00:37:33,790 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:33,790 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:33,790 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:33,790 | ^ 2025-09-09T00:37:33,791 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:33,791 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:33,791 | ^~~~~~~~ 2025-09-09T00:37:33,805 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:33,805 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:33,806 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:33,806 | ^ 2025-09-09T00:37:33,806 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:33,806 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:33,806 | ^~~~~~~~ 2025-09-09T00:37:33,811 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:33,811 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:33,811 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:33,811 | ^ 2025-09-09T00:37:33,812 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:33,812 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:33,812 | ^~~~~~~~ 2025-09-09T00:37:34,415 ./src/data.cpp: In member function ‘bool OpenBabel::OBResidueData::AssignBonds(OpenBabel::OBMol&, OpenBabel::OBBitVec&)’: 2025-09-09T00:37:34,415 ./src/data.cpp:810:56: warning: unused parameter ‘bv’ [-Wunused-parameter] 2025-09-09T00:37:34,416 810 | bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &bv) 2025-09-09T00:37:34,416 | ~~~~~~~~~~^~ 2025-09-09T00:37:37,737 In file included from ./src/data.cpp:21: 2025-09-09T00:37:37,737 In constructor ‘OpenBabel::OBElement::OBElement(int, const char*, double, double, double, int, double, double, double, double, double, double, double, std::string)’, 2025-09-09T00:37:37,737 inlined from ‘virtual void OpenBabel::OBElementTable::ParseLine(const char*)’ at ./src/data.cpp:117:79: 2025-09-09T00:37:37,737 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] 2025-09-09T00:37:37,737 118 | strncpy(_symbol, sym, 3); // Make sure to leave 4th character for null 2025-09-09T00:37:37,737 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:37:43,790 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/data.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:37:43,791 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/data.o /tmp/ccuShSUk.s 2025-09-09T00:37:43,796 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:44,922 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:37:44,923 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:37:44,923 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/data.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/data.' 2025-09-09T00:37:44,927 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/data_utilities.cpp -o build/temp.linux-armv7l-cpython-313/src/data_utilities.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:37:44,931 Using built-in specs. 2025-09-09T00:37:44,932 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:44,933 Target: arm-linux-gnueabihf 2025-09-09T00:37:44,933 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:37:44,933 Thread model: posix 2025-09-09T00:37:44,933 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:44,933 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:44,934 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/data_utilities.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:37:44,936 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/data_utilities.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase data_utilities.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cciK6tbv.s 2025-09-09T00:37:44,948 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:44,948 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:37:44,949 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:44,949 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:44,950 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:44,951 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:44,951 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:44,951 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:44,951 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:44,951 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:44,952 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:44,952 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:44,952 #include "..." search starts here: 2025-09-09T00:37:44,952 #include <...> search starts here: 2025-09-09T00:37:44,953 /usr/include/eigen3 2025-09-09T00:37:44,953 include 2025-09-09T00:37:44,953 /usr/include/python3.13 2025-09-09T00:37:44,953 /usr/include/c++/14 2025-09-09T00:37:44,953 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:44,954 /usr/include/c++/14/backward 2025-09-09T00:37:44,954 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:44,954 /usr/local/include 2025-09-09T00:37:44,954 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:44,954 /usr/include 2025-09-09T00:37:44,955 End of search list. 2025-09-09T00:37:44,976 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:46,441 In file included from include/openbabel/atom.h:33, 2025-09-09T00:37:46,441 from include/openbabel/mol.h:43, 2025-09-09T00:37:46,441 from include/openbabel/data_utilities.h:25, 2025-09-09T00:37:46,441 from ./src/data_utilities.cpp:23: 2025-09-09T00:37:46,442 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:46,442 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:46,442 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:46,442 | ^ 2025-09-09T00:37:46,442 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:46,442 37 | # define UNUSED(x) x 2025-09-09T00:37:46,442 | ^ 2025-09-09T00:37:47,056 In file included from include/openbabel/mol.h:52: 2025-09-09T00:37:47,056 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:47,056 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:47,056 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:47,056 | ^ 2025-09-09T00:37:47,056 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:47,056 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:47,057 | ^~~~~~~~ 2025-09-09T00:37:47,061 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:47,061 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:47,061 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:47,061 | ^ 2025-09-09T00:37:47,061 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:47,061 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:47,061 | ^~~~~~~~ 2025-09-09T00:37:47,076 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:47,076 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:47,076 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:47,076 | ^ 2025-09-09T00:37:47,077 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:47,077 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:47,077 | ^~~~~~~~ 2025-09-09T00:37:47,082 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:47,082 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:47,082 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:47,082 | ^ 2025-09-09T00:37:47,082 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:47,083 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:47,083 | ^~~~~~~~ 2025-09-09T00:37:47,347 ./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&)’: 2025-09-09T00:37:47,348 ./src/data_utilities.cpp:121:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:37:47,348 121 | for(int i = 0; (i search starts here: 2025-09-09T00:37:49,116 /usr/include/eigen3 2025-09-09T00:37:49,117 include 2025-09-09T00:37:49,117 /usr/include/python3.13 2025-09-09T00:37:49,117 /usr/include/c++/14 2025-09-09T00:37:49,117 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:49,117 /usr/include/c++/14/backward 2025-09-09T00:37:49,118 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:49,118 /usr/local/include 2025-09-09T00:37:49,118 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:49,118 /usr/include 2025-09-09T00:37:49,118 End of search list. 2025-09-09T00:37:49,140 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:50,304 In file included from ./src/depict/asciipainter.cpp:19: 2025-09-09T00:37:50,304 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:37:50,304 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:37:50,304 34 | void SetFontFamily(const std::string &fontFamily) {} 2025-09-09T00:37:50,304 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:37:50,314 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontSize(int)’: 2025-09-09T00:37:50,315 ./src/depict/asciipainter.cpp:54:38: warning: unused parameter ‘pointSize’ [-Wunused-parameter] 2025-09-09T00:37:50,315 54 | void ASCIIPainter::SetFontSize(int pointSize) 2025-09-09T00:37:50,315 | ~~~~^~~~~~~~~ 2025-09-09T00:37:50,315 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillColor(const OpenBabel::OBColor&)’: 2025-09-09T00:37:50,315 ./src/depict/asciipainter.cpp:58:50: warning: unused parameter ‘color’ [-Wunused-parameter] 2025-09-09T00:37:50,315 58 | void ASCIIPainter::SetFillColor(const OBColor &color) 2025-09-09T00:37:50,316 | ~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:37:50,316 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillRadial(const OpenBabel::OBColor&, const OpenBabel::OBColor&)’: 2025-09-09T00:37:50,316 ./src/depict/asciipainter.cpp:62:51: warning: unused parameter ‘start’ [-Wunused-parameter] 2025-09-09T00:37:50,316 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2025-09-09T00:37:50,316 | ~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:37:50,316 ./src/depict/asciipainter.cpp:62:73: warning: unused parameter ‘end’ [-Wunused-parameter] 2025-09-09T00:37:50,317 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2025-09-09T00:37:50,317 | ~~~~~~~~~~~~~~~^~~ 2025-09-09T00:37:50,317 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenColor(const OpenBabel::OBColor&)’: 2025-09-09T00:37:50,317 ./src/depict/asciipainter.cpp:67:49: warning: unused parameter ‘color’ [-Wunused-parameter] 2025-09-09T00:37:50,317 67 | void ASCIIPainter::SetPenColor(const OBColor &color) 2025-09-09T00:37:50,317 | ~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:37:50,318 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenWidth(double)’: 2025-09-09T00:37:50,318 ./src/depict/asciipainter.cpp:71:41: warning: unused parameter ‘width’ [-Wunused-parameter] 2025-09-09T00:37:50,318 71 | void ASCIIPainter::SetPenWidth(double width) 2025-09-09T00:37:50,318 | ~~~~~~~^~~~~ 2025-09-09T00:37:50,336 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawLine(double, double, double, double, const std::vector&)’: 2025-09-09T00:37:50,336 ./src/depict/asciipainter.cpp:80:103: warning: unused parameter ‘dashes’ [-Wunused-parameter] 2025-09-09T00:37:50,337 80 | void ASCIIPainter::DrawLine(double x1, double y1, double x2, double y2, const std::vector & dashes) 2025-09-09T00:37:50,337 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2025-09-09T00:37:50,353 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawCircle(double, double, double)’: 2025-09-09T00:37:50,353 ./src/depict/asciipainter.cpp:106:40: warning: unused parameter ‘x’ [-Wunused-parameter] 2025-09-09T00:37:50,353 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2025-09-09T00:37:50,353 | ~~~~~~~^ 2025-09-09T00:37:50,353 ./src/depict/asciipainter.cpp:106:50: warning: unused parameter ‘y’ [-Wunused-parameter] 2025-09-09T00:37:50,354 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2025-09-09T00:37:50,354 | ~~~~~~~^ 2025-09-09T00:37:50,354 ./src/depict/asciipainter.cpp:106:60: warning: unused parameter ‘r’ [-Wunused-parameter] 2025-09-09T00:37:50,354 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2025-09-09T00:37:50,354 | ~~~~~~~^ 2025-09-09T00:37:50,354 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawBall(double, double, double, double)’: 2025-09-09T00:37:50,355 ./src/depict/asciipainter.cpp:110:38: warning: unused parameter ‘x’ [-Wunused-parameter] 2025-09-09T00:37:50,355 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:37:50,355 | ~~~~~~~^ 2025-09-09T00:37:50,355 ./src/depict/asciipainter.cpp:110:48: warning: unused parameter ‘y’ [-Wunused-parameter] 2025-09-09T00:37:50,355 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:37:50,355 | ~~~~~~~^ 2025-09-09T00:37:50,355 ./src/depict/asciipainter.cpp:110:58: warning: unused parameter ‘r’ [-Wunused-parameter] 2025-09-09T00:37:50,355 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:37:50,356 | ~~~~~~~^ 2025-09-09T00:37:50,356 ./src/depict/asciipainter.cpp:110:68: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2025-09-09T00:37:50,356 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:37:50,356 | ~~~~~~~^~~~~~~ 2025-09-09T00:37:50,357 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawText(double, double, const std::string&)’: 2025-09-09T00:37:50,357 ./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] 2025-09-09T00:37:50,357 118 | for (int i=0; i search starts here: 2025-09-09T00:37:52,366 /usr/include/eigen3 2025-09-09T00:37:52,366 include 2025-09-09T00:37:52,366 /usr/include/python3.13 2025-09-09T00:37:52,367 /usr/include/c++/14 2025-09-09T00:37:52,367 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:52,367 /usr/include/c++/14/backward 2025-09-09T00:37:52,367 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:52,367 /usr/local/include 2025-09-09T00:37:52,367 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:52,368 /usr/include 2025-09-09T00:37:52,368 End of search list. 2025-09-09T00:37:52,387 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:53,542 In file included from ./src/depict/commandpainter.cpp:19: 2025-09-09T00:37:53,542 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:37:53,542 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:37:53,542 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2025-09-09T00:37:53,542 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:37:53,582 ./src/depict/commandpainter.cpp: In member function ‘virtual void OpenBabel::CommandPainter::DrawBall(double, double, double, double)’: 2025-09-09T00:37:53,582 ./src/depict/commandpainter.cpp:115:70: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2025-09-09T00:37:53,582 115 | void CommandPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:37:53,582 | ~~~~~~~^~~~~~~ 2025-09-09T00:37:53,585 ./src/depict/commandpainter.cpp: In member function ‘virtual OpenBabel::OBFontMetrics OpenBabel::CommandPainter::GetFontMetrics(const std::string&)’: 2025-09-09T00:37:53,585 ./src/depict/commandpainter.cpp:125:67: warning: unused parameter ‘text’ [-Wunused-parameter] 2025-09-09T00:37:53,585 125 | OBFontMetrics CommandPainter::GetFontMetrics(const std::string &text) 2025-09-09T00:37:53,586 | ~~~~~~~~~~~~~~~~~~~^~~~ 2025-09-09T00:37:54,185 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/commandpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/' 2025-09-09T00:37:54,186 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/depict/commandpainter.o /tmp/ccGIiPCG.s 2025-09-09T00:37:54,191 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:54,270 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:37:54,270 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:37:54,271 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/commandpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/commandpainter.' 2025-09-09T00:37:54,272 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/depict/depict.cpp -o build/temp.linux-armv7l-cpython-313/src/depict/depict.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:37:54,276 Using built-in specs. 2025-09-09T00:37:54,277 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:54,277 Target: arm-linux-gnueabihf 2025-09-09T00:37:54,277 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:37:54,278 Thread model: posix 2025-09-09T00:37:54,278 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:54,278 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:54,278 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/depict.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/' 2025-09-09T00:37:54,280 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/depict/depict.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/depict/ -dumpbase depict.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccywd5wh.s 2025-09-09T00:37:54,293 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:54,293 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:37:54,293 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:54,294 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:54,294 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:54,295 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:54,295 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:54,295 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:54,295 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:54,296 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:54,296 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:54,296 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:54,296 #include "..." search starts here: 2025-09-09T00:37:54,296 #include <...> search starts here: 2025-09-09T00:37:54,296 /usr/include/eigen3 2025-09-09T00:37:54,297 include 2025-09-09T00:37:54,297 /usr/include/python3.13 2025-09-09T00:37:54,297 /usr/include/c++/14 2025-09-09T00:37:54,297 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:54,297 /usr/include/c++/14/backward 2025-09-09T00:37:54,297 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:54,298 /usr/local/include 2025-09-09T00:37:54,298 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:54,298 /usr/include 2025-09-09T00:37:54,298 End of search list. 2025-09-09T00:37:54,315 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:55,845 In file included from include/openbabel/atom.h:33, 2025-09-09T00:37:55,846 from include/openbabel/mol.h:43, 2025-09-09T00:37:55,846 from ./src/depict/depict.cpp:20: 2025-09-09T00:37:55,846 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:55,846 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:55,846 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:55,846 | ^ 2025-09-09T00:37:55,846 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:55,846 37 | # define UNUSED(x) x 2025-09-09T00:37:55,846 | ^ 2025-09-09T00:37:56,468 In file included from include/openbabel/mol.h:52: 2025-09-09T00:37:56,469 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:56,469 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:56,469 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:56,469 | ^ 2025-09-09T00:37:56,469 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:56,469 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:56,469 | ^~~~~~~~ 2025-09-09T00:37:56,473 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:56,474 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:56,474 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:56,474 | ^ 2025-09-09T00:37:56,474 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:56,474 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:56,474 | ^~~~~~~~ 2025-09-09T00:37:56,489 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:56,489 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:56,489 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:56,489 | ^ 2025-09-09T00:37:56,489 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:56,490 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:56,490 | ^~~~~~~~ 2025-09-09T00:37:56,495 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:56,495 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:56,495 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:56,495 | ^ 2025-09-09T00:37:56,495 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:56,495 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:56,495 | ^~~~~~~~ 2025-09-09T00:37:56,999 ./src/depict/depict.cpp: In function ‘unsigned int OpenBabel::GetAtomSymClass(OBAtom*)’: 2025-09-09T00:37:56,999 ./src/depict/depict.cpp:280:11: warning: unused variable ‘nclasses’ [-Wunused-variable] 2025-09-09T00:37:56,999 280 | int nclasses = end_pos - copy_sym.begin(); 2025-09-09T00:37:56,999 | ^~~~~~~~ 2025-09-09T00:37:57,140 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtom(OpenBabel::OBAtom*)’: 2025-09-09T00:37:57,140 ./src/depict/depict.cpp:839:42: warning: unused parameter ‘atom’ [-Wunused-parameter] 2025-09-09T00:37:57,140 839 | void OBDepictPrivate::DrawAtom(OBAtom *atom) 2025-09-09T00:37:57,140 | ~~~~~~~~^~~~ 2025-09-09T00:37:57,148 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtomLabel(const std::string&, int, const OpenBabel::vector3&)’: 2025-09-09T00:37:57,148 ./src/depict/depict.cpp:966:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:37:57,148 966 | OBFontMetrics metrics = painter->GetFontMetrics(str); 2025-09-09T00:37:57,148 | ^~~~~~~ 2025-09-09T00:37:57,150 ./src/depict/depict.cpp:971:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:37:57,150 971 | OBFontMetrics metrics = painter->GetFontMetrics(subscript); 2025-09-09T00:37:57,150 | ^~~~~~~ 2025-09-09T00:37:57,160 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawSimpleBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, int, bool)’: 2025-09-09T00:37:57,161 ./src/depict/depict.cpp:1011:36: warning: unused parameter ‘crossed_bond’ [-Wunused-parameter] 2025-09-09T00:37:57,161 1011 | OBAtom* endAtom, int order, bool crossed_bond) 2025-09-09T00:37:57,161 | ~~~~~^~~~~~~~~~~~ 2025-09-09T00:37:57,179 ./src/depict/depict.cpp: In member function ‘void OpenBabel::OBDepictPrivateBallAndStick::DrawAromaticRingBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, const OpenBabel::vector3&, double)’: 2025-09-09T00:37:57,179 ./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] 2025-09-09T00:37:57,179 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2025-09-09T00:37:57,179 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2025-09-09T00:37:57,179 ./src/depict/depict.cpp:1156:100: note: add parentheses around ‘sizeof (double)’ to silence this warning 2025-09-09T00:37:57,180 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2025-09-09T00:37:57,180 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:57,180 | ( ) 2025-09-09T00:37:57,180 ./src/depict/depict.cpp:1155:24: note: array ‘dashpattern’ declared here 2025-09-09T00:37:57,180 1155 | static const float dashpattern[] = {5., 5.}; 2025-09-09T00:37:57,180 | ^~~~~~~~~~~ 2025-09-09T00:37:57,181 ./src/depict/depict.cpp:1133:152: warning: unused parameter ‘center’ [-Wunused-parameter] 2025-09-09T00:37:57,182 1133 | inline void OBDepictPrivateBallAndStick::DrawAromaticRingBond(OBAtom *prevAtom, OBAtom *beginAtom, OBAtom *endAtom, OBAtom *nextAtom, const vector3 ¢er, double dist) 2025-09-09T00:37:57,182 | ~~~~~~~~~~~~~~~^~~~~~ 2025-09-09T00:38:04,016 In file included from /usr/include/c++/14/algorithm:61, 2025-09-09T00:38:04,016 from include/openbabel/ring.h:24, 2025-09-09T00:38:04,016 from include/openbabel/mol.h:51: 2025-09-09T00:38:04,016 /usr/include/c++/14/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&)>]’: 2025-09-09T00:38:04,016 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,017 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:38:04,017 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:04,017 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,047 /usr/include/c++/14/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&)>]’: 2025-09-09T00:38:04,048 /usr/include/c++/14/bits/stl_algo.h:85:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,048 85 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, 2025-09-09T00:38:04,048 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:04,048 /usr/include/c++/14/bits/stl_algo.h:85:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,048 /usr/include/c++/14/bits/stl_algo.h:85:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,048 /usr/include/c++/14/bits/stl_algo.h:85:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,095 In file included from /usr/include/c++/14/bits/stl_algo.h:61: 2025-09-09T00:38:04,095 /usr/include/c++/14/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&)>]’: 2025-09-09T00:38:04,095 /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,095 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:38:04,096 | ^~~~~~~~~~~~~ 2025-09-09T00:38:04,159 /usr/include/c++/14/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&)>]’: 2025-09-09T00:38:04,160 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,160 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:38:04,160 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:04,160 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,161 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&)>]’, 2025-09-09T00:38:04,161 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++/14/bits/stl_algo.h:1889:38: 2025-09-09T00:38:04,161 /usr/include/c++/14/bits/stl_algo.h:1855:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,162 1855 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2025-09-09T00:38:04,162 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:04,162 1856 | __comp); 2025-09-09T00:38:04,162 | ~~~~~~~ 2025-09-09T00:38:04,162 /usr/include/c++/14/bits/stl_algo.h:1855:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,163 /usr/include/c++/14/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&)>]’: 2025-09-09T00:38:04,163 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:04,163 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:38:04,163 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:04,974 ./src/depict/depict.cpp: In member function ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’: 2025-09-09T00:38:04,974 ./src/depict/depict.cpp:420:22: warning: ‘min_x’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:04,974 420 | width = max_x - min_x + 2*margin; 2025-09-09T00:38:04,974 | ~~~~~~^~~~~~~ 2025-09-09T00:38:04,974 ./src/depict/depict.cpp:393:14: note: ‘min_x’ was declared here 2025-09-09T00:38:04,975 393 | double min_x, max_x; 2025-09-09T00:38:04,975 | ^~~~~ 2025-09-09T00:38:04,975 ./src/depict/depict.cpp:420:22: warning: ‘max_x’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:04,975 420 | width = max_x - min_x + 2*margin; 2025-09-09T00:38:04,975 | ~~~~~~^~~~~~~ 2025-09-09T00:38:04,975 ./src/depict/depict.cpp:393:21: note: ‘max_x’ was declared here 2025-09-09T00:38:04,975 393 | double min_x, max_x; 2025-09-09T00:38:04,976 | ^~~~~ 2025-09-09T00:38:04,976 ./src/depict/depict.cpp:421:22: warning: ‘min_y’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:04,976 421 | height = max_y - min_y + 2*margin; 2025-09-09T00:38:04,976 | ~~~~~~^~~~~~~ 2025-09-09T00:38:04,976 ./src/depict/depict.cpp:394:14: note: ‘min_y’ was declared here 2025-09-09T00:38:04,976 394 | double min_y, max_y; 2025-09-09T00:38:04,976 | ^~~~~ 2025-09-09T00:38:04,977 ./src/depict/depict.cpp:421:22: warning: ‘max_y’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:04,977 421 | height = max_y - min_y + 2*margin; 2025-09-09T00:38:04,977 | ~~~~~~^~~~~~~ 2025-09-09T00:38:04,977 ./src/depict/depict.cpp:394:21: note: ‘max_y’ was declared here 2025-09-09T00:38:04,977 394 | double min_y, max_y; 2025-09-09T00:38:04,977 | ^~~~~ 2025-09-09T00:38:04,977 ./src/depict/depict.cpp:423:25: warning: ‘min_z’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:04,977 423 | d->zScale = max_z - min_z; 2025-09-09T00:38:04,978 | ~~~~~~^~~~~~~ 2025-09-09T00:38:04,978 ./src/depict/depict.cpp:395:14: note: ‘min_z’ was declared here 2025-09-09T00:38:04,978 395 | double min_z, max_z; 2025-09-09T00:38:04,978 | ^~~~~ 2025-09-09T00:38:04,978 ./src/depict/depict.cpp:423:25: warning: ‘max_z’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:04,978 423 | d->zScale = max_z - min_z; 2025-09-09T00:38:04,978 | ~~~~~~^~~~~~~ 2025-09-09T00:38:04,978 ./src/depict/depict.cpp:395:21: note: ‘max_z’ was declared here 2025-09-09T00:38:04,979 395 | double min_z, max_z; 2025-09-09T00:38:04,979 | ^~~~~ 2025-09-09T00:38:05,018 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&)>]’, 2025-09-09T00:38:05,018 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++/14/bits/stl_algo.h:1889:38, 2025-09-09T00:38:05,018 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++/14/bits/stl_algo.h:1905:25, 2025-09-09T00:38:05,019 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++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:38:05,019 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2025-09-09T00:38:05,019 /usr/include/c++/14/bits/stl_algo.h:1855:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:05,019 1855 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2025-09-09T00:38:05,019 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,019 1856 | __comp); 2025-09-09T00:38:05,019 | ~~~~~~~ 2025-09-09T00:38:05,019 /usr/include/c++/14/bits/stl_algo.h:1855:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:05,020 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&)>]’, 2025-09-09T00:38:05,020 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++/14/bits/stl_algo.h:1905:25, 2025-09-09T00:38:05,020 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++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:38:05,020 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2025-09-09T00:38:05,021 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:05,021 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:38:05,021 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,021 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&)>]’, 2025-09-09T00:38:05,021 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++/14/bits/stl_algo.h:1908:31, 2025-09-09T00:38:05,022 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++/14/bits/stl_algo.h:4805:18, 2025-09-09T00:38:05,022 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2025-09-09T00:38:05,022 /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:05,022 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:38:05,022 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,032 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T00:38:05,032 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:38:05,032 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:06,653 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/depict.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/' 2025-09-09T00:38:06,654 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/depict/depict.o /tmp/ccywd5wh.s 2025-09-09T00:38:06,662 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:07,490 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:07,490 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:07,490 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/depict.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/depict.' 2025-09-09T00:38:07,491 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/depict/svgpainter.cpp -o build/temp.linux-armv7l-cpython-313/src/depict/svgpainter.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:07,495 Using built-in specs. 2025-09-09T00:38:07,497 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:07,497 Target: arm-linux-gnueabihf 2025-09-09T00:38:07,497 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:07,497 Thread model: posix 2025-09-09T00:38:07,497 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:07,498 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:07,498 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/svgpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/' 2025-09-09T00:38:07,500 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/depict/svgpainter.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/depict/ -dumpbase svgpainter.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccT1FTfP.s 2025-09-09T00:38:07,513 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:07,513 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:07,513 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:07,513 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:07,515 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:07,515 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:07,516 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:07,516 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:07,516 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:07,516 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:07,516 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:07,516 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:07,517 #include "..." search starts here: 2025-09-09T00:38:07,517 #include <...> search starts here: 2025-09-09T00:38:07,517 /usr/include/eigen3 2025-09-09T00:38:07,517 include 2025-09-09T00:38:07,517 /usr/include/python3.13 2025-09-09T00:38:07,517 /usr/include/c++/14 2025-09-09T00:38:07,517 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:07,518 /usr/include/c++/14/backward 2025-09-09T00:38:07,518 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:07,518 /usr/local/include 2025-09-09T00:38:07,518 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:07,518 /usr/include 2025-09-09T00:38:07,518 End of search list. 2025-09-09T00:38:07,535 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:08,905 In file included from ./src/depict/svgpainter.cpp:18: 2025-09-09T00:38:08,905 include/openbabel/depict/svgpainter.h: In constructor ‘OpenBabel::SVGPainter::SVGPainter(std::ostream&, std::set >*, bool, double, double)’: 2025-09-09T00:38:08,905 include/openbabel/depict/svgpainter.h:77:11: warning: ‘OpenBabel::SVGPainter::m_fontPointSize’ will be initialized after [-Wreorder] 2025-09-09T00:38:08,905 77 | int m_fontPointSize; 2025-09-09T00:38:08,905 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:08,905 include/openbabel/depict/svgpainter.h:75:12: warning: ‘bool OpenBabel::SVGPainter::m_isFillcolor’ [-Wreorder] 2025-09-09T00:38:08,905 75 | bool m_isFillcolor; 2025-09-09T00:38:08,905 | ^~~~~~~~~~~~~ 2025-09-09T00:38:08,906 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2025-09-09T00:38:08,906 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2025-09-09T00:38:08,906 | ^~~~~~~~~~ 2025-09-09T00:38:08,906 include/openbabel/depict/svgpainter.h:75:12: warning: ‘OpenBabel::SVGPainter::m_isFillcolor’ will be initialized after [-Wreorder] 2025-09-09T00:38:08,906 75 | bool m_isFillcolor; 2025-09-09T00:38:08,906 | ^~~~~~~~~~~~~ 2025-09-09T00:38:08,907 include/openbabel/depict/svgpainter.h:74:32: warning: ‘std::set >* OpenBabel::SVGPainter::m_Gradients’ [-Wreorder] 2025-09-09T00:38:08,907 74 | std::set *m_Gradients; 2025-09-09T00:38:08,907 | ^~~~~~~~~~~ 2025-09-09T00:38:08,907 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2025-09-09T00:38:08,907 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2025-09-09T00:38:08,907 | ^~~~~~~~~~ 2025-09-09T00:38:08,980 ./src/depict/svgpainter.cpp: In member function ‘void OpenBabel::SVGPainter::WriteImage(const std::string&)’: 2025-09-09T00:38:08,980 ./src/depict/svgpainter.cpp:172:50: warning: unused parameter ‘filename’ [-Wunused-parameter] 2025-09-09T00:38:08,980 172 | void SVGPainter::WriteImage(const std::string &filename) 2025-09-09T00:38:08,980 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:38:10,723 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/svgpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/' 2025-09-09T00:38:10,724 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/depict/svgpainter.o /tmp/ccT1FTfP.s 2025-09-09T00:38:10,729 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:10,929 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:10,930 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:10,930 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/depict/svgpainter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/depict/svgpainter.' 2025-09-09T00:38:10,932 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/descriptor.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptor.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:10,936 Using built-in specs. 2025-09-09T00:38:10,937 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:10,937 Target: arm-linux-gnueabihf 2025-09-09T00:38:10,938 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:10,938 Thread model: posix 2025-09-09T00:38:10,938 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:10,938 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:10,939 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:10,940 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptor.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase descriptor.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc2tldjL.s 2025-09-09T00:38:10,953 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:10,954 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:10,954 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:10,954 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:10,955 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:10,955 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:10,955 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:10,956 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:10,956 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:10,956 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:10,956 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:10,956 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:10,957 #include "..." search starts here: 2025-09-09T00:38:10,957 #include <...> search starts here: 2025-09-09T00:38:10,957 /usr/include/eigen3 2025-09-09T00:38:10,957 include 2025-09-09T00:38:10,957 /usr/include/python3.13 2025-09-09T00:38:10,957 /usr/include/c++/14 2025-09-09T00:38:10,958 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:10,958 /usr/include/c++/14/backward 2025-09-09T00:38:10,958 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:10,958 /usr/local/include 2025-09-09T00:38:10,958 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:10,958 /usr/include 2025-09-09T00:38:10,959 End of search list. 2025-09-09T00:38:10,975 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:12,527 In file included from include/openbabel/generic.h:31, 2025-09-09T00:38:12,527 from ./src/descriptor.cpp:21: 2025-09-09T00:38:12,527 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:12,527 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:12,527 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:12,527 | ^ 2025-09-09T00:38:12,528 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:12,528 37 | # define UNUSED(x) x 2025-09-09T00:38:12,528 | ^ 2025-09-09T00:38:12,684 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:12,684 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:12,684 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:12,684 | ^ 2025-09-09T00:38:12,684 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:12,684 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:12,684 | ^~~~~~~~ 2025-09-09T00:38:12,688 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:12,689 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:12,689 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:12,689 | ^ 2025-09-09T00:38:12,689 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:12,689 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:12,689 | ^~~~~~~~ 2025-09-09T00:38:12,703 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:12,704 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:12,704 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:12,704 | ^ 2025-09-09T00:38:12,704 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:12,704 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:12,704 | ^~~~~~~~ 2025-09-09T00:38:12,709 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:12,709 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:12,710 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:12,710 | ^ 2025-09-09T00:38:12,710 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:12,710 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:12,710 | ^~~~~~~~ 2025-09-09T00:38:12,779 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:38:12,779 from ./src/descriptor.cpp:23: 2025-09-09T00:38:12,779 include/openbabel/plugin.h: At global scope: 2025-09-09T00:38:12,779 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:12,779 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:12,779 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:12,780 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:38:12,780 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:38:12,780 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:38:12,780 from /usr/include/c++/14/ios:44, 2025-09-09T00:38:12,780 from /usr/include/c++/14/istream:40, 2025-09-09T00:38:12,781 from /usr/include/c++/14/sstream:40, 2025-09-09T00:38:12,781 from include/openbabel/oberror.h:26, 2025-09-09T00:38:12,781 from ./src/descriptor.cpp:20: 2025-09-09T00:38:12,781 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:12,781 131 | struct binary_function 2025-09-09T00:38:12,781 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:16,220 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:16,220 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/descriptor.o /tmp/cc2tldjL.s 2025-09-09T00:38:16,225 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:16,567 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:16,568 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:16,568 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptor.' 2025-09-09T00:38:16,570 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/descriptors/cansmidescriptor.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptors/cansmidescriptor.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:16,574 Using built-in specs. 2025-09-09T00:38:16,575 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:16,576 Target: arm-linux-gnueabihf 2025-09-09T00:38:16,576 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:16,576 Thread model: posix 2025-09-09T00:38:16,576 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:16,576 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:16,577 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cansmidescriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:16,579 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/cansmidescriptor.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/descriptors/ -dumpbase cansmidescriptor.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccRGRMYg.s 2025-09-09T00:38:16,592 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:16,592 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:16,593 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:16,593 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:16,594 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:16,594 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:16,594 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:16,595 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:16,595 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:16,595 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:16,595 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:16,595 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:16,596 #include "..." search starts here: 2025-09-09T00:38:16,596 #include <...> search starts here: 2025-09-09T00:38:16,596 /usr/include/eigen3 2025-09-09T00:38:16,596 include 2025-09-09T00:38:16,596 /usr/include/python3.13 2025-09-09T00:38:16,597 /usr/include/c++/14 2025-09-09T00:38:16,597 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:16,597 /usr/include/c++/14/backward 2025-09-09T00:38:16,597 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:16,597 /usr/local/include 2025-09-09T00:38:16,597 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:16,598 /usr/include 2025-09-09T00:38:16,598 End of search list. 2025-09-09T00:38:16,615 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:17,975 In file included from include/openbabel/format.h:22, 2025-09-09T00:38:17,975 from include/openbabel/obconversion.h:37, 2025-09-09T00:38:17,975 from ./src/descriptors/cansmidescriptor.cpp:22: 2025-09-09T00:38:17,975 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:17,975 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:17,975 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:17,976 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:38:17,976 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:38:17,976 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:38:17,976 from /usr/include/c++/14/ios:44, 2025-09-09T00:38:17,976 from /usr/include/c++/14/istream:40, 2025-09-09T00:38:17,976 from /usr/include/c++/14/sstream:40, 2025-09-09T00:38:17,977 from include/openbabel/oberror.h:26, 2025-09-09T00:38:17,977 from ./src/descriptors/cansmidescriptor.cpp:20: 2025-09-09T00:38:17,977 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:17,977 131 | struct binary_function 2025-09-09T00:38:17,977 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:18,119 ./src/descriptors/cansmidescriptor.cpp: In member function ‘virtual bool OpenBabel::CanSmiles::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2025-09-09T00:38:18,119 ./src/descriptors/cansmidescriptor.cpp:42:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:38:18,120 42 | bool CanSmiles::Compare(OBBase* pOb, istream& optionText, bool noEval, string* param) 2025-09-09T00:38:18,120 | ~~~~~~~~^~~~~ 2025-09-09T00:38:19,191 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cansmidescriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:19,192 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/descriptors/cansmidescriptor.o /tmp/ccRGRMYg.s 2025-09-09T00:38:19,197 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:19,318 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:19,318 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:19,319 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cansmidescriptor.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cansmidescriptor.' 2025-09-09T00:38:19,320 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/descriptors/cmpdfilter.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptors/cmpdfilter.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:19,324 Using built-in specs. 2025-09-09T00:38:19,325 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:19,325 Target: arm-linux-gnueabihf 2025-09-09T00:38:19,326 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:19,326 Thread model: posix 2025-09-09T00:38:19,326 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:19,326 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:19,326 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cmpdfilter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:19,328 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/cmpdfilter.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/descriptors/ -dumpbase cmpdfilter.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccUEXBia.s 2025-09-09T00:38:19,341 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:19,341 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:19,342 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:19,342 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:19,343 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:19,343 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:19,343 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:19,344 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:19,344 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:19,344 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:19,344 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:19,344 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:19,345 #include "..." search starts here: 2025-09-09T00:38:19,345 #include <...> search starts here: 2025-09-09T00:38:19,345 /usr/include/eigen3 2025-09-09T00:38:19,345 include 2025-09-09T00:38:19,345 /usr/include/python3.13 2025-09-09T00:38:19,346 /usr/include/c++/14 2025-09-09T00:38:19,346 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:19,346 /usr/include/c++/14/backward 2025-09-09T00:38:19,346 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:19,346 /usr/local/include 2025-09-09T00:38:19,347 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:19,347 /usr/include 2025-09-09T00:38:19,347 End of search list. 2025-09-09T00:38:19,364 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:20,646 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:38:20,646 from ./src/descriptors/cmpdfilter.cpp:21: 2025-09-09T00:38:20,647 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:20,647 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:20,647 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:20,648 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:38:20,648 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:38:20,648 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:38:20,648 from /usr/include/c++/14/ios:44, 2025-09-09T00:38:20,648 from /usr/include/c++/14/istream:40, 2025-09-09T00:38:20,648 from /usr/include/c++/14/sstream:40, 2025-09-09T00:38:20,648 from include/openbabel/oberror.h:26, 2025-09-09T00:38:20,648 from ./src/descriptors/cmpdfilter.cpp:20: 2025-09-09T00:38:20,648 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:20,648 131 | struct binary_function 2025-09-09T00:38:20,648 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:20,693 ./src/descriptors/cmpdfilter.cpp: In member function ‘virtual bool OpenBabel::CompoundFilter::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2025-09-09T00:38:20,694 ./src/descriptors/cmpdfilter.cpp:74:68: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:38:20,694 74 | virtual bool Compare(OBBase* pOb, istream&, bool noEval, string* param) 2025-09-09T00:38:20,694 | ~~~~~~~~^~~~~ 2025-09-09T00:38:22,023 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cmpdfilter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:22,024 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/descriptors/cmpdfilter.o /tmp/ccUEXBia.s 2025-09-09T00:38:22,029 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:22,168 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:22,168 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:22,169 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cmpdfilter.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/cmpdfilter.' 2025-09-09T00:38:22,170 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/descriptors/filters.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptors/filters.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:22,175 Using built-in specs. 2025-09-09T00:38:22,176 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:22,176 Target: arm-linux-gnueabihf 2025-09-09T00:38:22,176 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:22,177 Thread model: posix 2025-09-09T00:38:22,177 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:22,177 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:22,177 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/filters.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:22,179 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/filters.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/descriptors/ -dumpbase filters.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccNKSoGU.s 2025-09-09T00:38:22,190 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:22,190 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:22,190 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:22,190 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:22,191 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:22,191 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:22,192 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:22,192 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:22,192 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:22,192 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:22,193 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:22,193 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:22,193 #include "..." search starts here: 2025-09-09T00:38:22,193 #include <...> search starts here: 2025-09-09T00:38:22,193 /usr/include/eigen3 2025-09-09T00:38:22,194 include 2025-09-09T00:38:22,194 /usr/include/python3.13 2025-09-09T00:38:22,194 /usr/include/c++/14 2025-09-09T00:38:22,194 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:22,194 /usr/include/c++/14/backward 2025-09-09T00:38:22,194 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:22,195 /usr/local/include 2025-09-09T00:38:22,195 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:22,195 /usr/include 2025-09-09T00:38:22,195 End of search list. 2025-09-09T00:38:22,215 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:23,772 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:23,772 from include/openbabel/mol.h:43, 2025-09-09T00:38:23,772 from ./src/descriptors/filters.cpp:21: 2025-09-09T00:38:23,772 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:23,772 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:23,772 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:23,772 | ^ 2025-09-09T00:38:23,772 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:23,772 37 | # define UNUSED(x) x 2025-09-09T00:38:23,773 | ^ 2025-09-09T00:38:24,320 In file included from include/openbabel/mol.h:52: 2025-09-09T00:38:24,320 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:24,320 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:24,320 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:24,320 | ^ 2025-09-09T00:38:24,321 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:24,321 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:24,321 | ^~~~~~~~ 2025-09-09T00:38:24,325 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:24,325 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:24,325 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:24,325 | ^ 2025-09-09T00:38:24,325 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:24,325 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:24,326 | ^~~~~~~~ 2025-09-09T00:38:24,340 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:24,340 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:24,340 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:24,340 | ^ 2025-09-09T00:38:24,341 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:24,341 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:24,341 | ^~~~~~~~ 2025-09-09T00:38:24,346 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:24,346 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:24,346 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:24,346 | ^ 2025-09-09T00:38:24,347 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:24,347 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:24,347 | ^~~~~~~~ 2025-09-09T00:38:24,485 In file included from include/openbabel/format.h:22, 2025-09-09T00:38:24,485 from include/openbabel/obconversion.h:37, 2025-09-09T00:38:24,485 from ./src/descriptors/filters.cpp:22: 2025-09-09T00:38:24,485 include/openbabel/plugin.h: At global scope: 2025-09-09T00:38:24,486 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:24,486 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:24,486 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:24,486 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:38:24,487 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:38:24,487 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:38:24,487 from /usr/include/c++/14/ios:44, 2025-09-09T00:38:24,487 from /usr/include/c++/14/istream:40, 2025-09-09T00:38:24,487 from /usr/include/c++/14/sstream:40, 2025-09-09T00:38:24,487 from include/openbabel/oberror.h:26, 2025-09-09T00:38:24,487 from ./src/descriptors/filters.cpp:20: 2025-09-09T00:38:24,487 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:24,487 131 | struct binary_function 2025-09-09T00:38:24,487 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:24,649 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::MWFilter::Predict(OpenBabel::OBBase*, std::string*)’: 2025-09-09T00:38:24,649 ./src/descriptors/filters.cpp:36:47: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:38:24,649 36 | virtual double Predict(OBBase* pOb, string* param=NULL) 2025-09-09T00:38:24,649 | ^ 2025-09-09T00:38:24,657 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::FormulaDescriptor::GetStringValue(OpenBabel::OBBase*, std::string&, std::string*)’: 2025-09-09T00:38:24,657 ./src/descriptors/filters.cpp:142:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:38:24,658 142 | virtual double GetStringValue(OBBase* pOb, std::string& svalue, std::string* param=NULL) 2025-09-09T00:38:24,658 | ^ 2025-09-09T00:38:26,706 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/filters.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:26,707 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/descriptors/filters.o /tmp/ccNKSoGU.s 2025-09-09T00:38:26,712 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:26,871 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:26,871 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:26,871 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/filters.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/filters.' 2025-09-09T00:38:26,873 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/descriptors/groupcontrib.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptors/groupcontrib.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:26,877 Using built-in specs. 2025-09-09T00:38:26,878 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:26,878 Target: arm-linux-gnueabihf 2025-09-09T00:38:26,878 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:26,879 Thread model: posix 2025-09-09T00:38:26,879 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:26,879 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:26,879 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/groupcontrib.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:26,881 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/groupcontrib.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/descriptors/ -dumpbase groupcontrib.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccHUH0VB.s 2025-09-09T00:38:26,891 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:26,892 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:26,892 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:26,892 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:26,893 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:26,894 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:26,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:26,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:26,894 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:26,894 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:26,895 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:26,895 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:26,895 #include "..." search starts here: 2025-09-09T00:38:26,895 #include <...> search starts here: 2025-09-09T00:38:26,895 /usr/include/eigen3 2025-09-09T00:38:26,896 include 2025-09-09T00:38:26,896 /usr/include/python3.13 2025-09-09T00:38:26,896 /usr/include/c++/14 2025-09-09T00:38:26,896 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:26,896 /usr/include/c++/14/backward 2025-09-09T00:38:26,897 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:26,897 /usr/local/include 2025-09-09T00:38:26,897 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:26,897 /usr/include 2025-09-09T00:38:26,897 End of search list. 2025-09-09T00:38:26,916 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:28,412 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:28,412 from include/openbabel/mol.h:43, 2025-09-09T00:38:28,413 from ./src/descriptors/groupcontrib.cpp:27: 2025-09-09T00:38:28,413 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:28,413 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:28,413 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:28,413 | ^ 2025-09-09T00:38:28,413 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:28,413 37 | # define UNUSED(x) x 2025-09-09T00:38:28,413 | ^ 2025-09-09T00:38:29,027 In file included from include/openbabel/mol.h:52: 2025-09-09T00:38:29,027 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:29,027 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:29,027 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:29,027 | ^ 2025-09-09T00:38:29,027 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:29,028 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:29,028 | ^~~~~~~~ 2025-09-09T00:38:29,032 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:29,032 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:29,032 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:29,032 | ^ 2025-09-09T00:38:29,032 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:29,032 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:29,032 | ^~~~~~~~ 2025-09-09T00:38:29,047 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:29,047 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:29,047 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:29,047 | ^ 2025-09-09T00:38:29,048 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:29,048 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:29,048 | ^~~~~~~~ 2025-09-09T00:38:29,053 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:29,053 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:29,053 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:29,053 | ^ 2025-09-09T00:38:29,053 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:29,054 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:29,054 | ^~~~~~~~ 2025-09-09T00:38:29,230 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:38:29,230 from include/openbabel/groupcontrib.h:28, 2025-09-09T00:38:29,230 from ./src/descriptors/groupcontrib.cpp:29: 2025-09-09T00:38:29,230 include/openbabel/plugin.h: At global scope: 2025-09-09T00:38:29,230 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:29,230 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:29,230 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:29,231 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:38:29,231 from /usr/include/c++/14/vector:68, 2025-09-09T00:38:29,232 from ./src/descriptors/groupcontrib.cpp:25: 2025-09-09T00:38:29,232 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:29,232 131 | struct binary_function 2025-09-09T00:38:29,232 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:29,445 ./src/descriptors/groupcontrib.cpp: In member function ‘virtual double OpenBabel::OBGroupContrib::Predict(OpenBabel::OBBase*, std::string*)’: 2025-09-09T00:38:29,445 ./src/descriptors/groupcontrib.cpp:106:55: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:38:29,445 106 | double OBGroupContrib::Predict(OBBase* pOb, string* param) 2025-09-09T00:38:29,445 | ~~~~~~~~^~~~~ 2025-09-09T00:38:33,294 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/groupcontrib.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:33,294 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/descriptors/groupcontrib.o /tmp/ccHUH0VB.s 2025-09-09T00:38:33,300 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:33,645 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:33,646 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:33,646 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/groupcontrib.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/groupcontrib.' 2025-09-09T00:38:33,648 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/descriptors/smartsdescriptors.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptors/smartsdescriptors.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:33,652 Using built-in specs. 2025-09-09T00:38:33,653 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:33,653 Target: arm-linux-gnueabihf 2025-09-09T00:38:33,654 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:33,654 Thread model: posix 2025-09-09T00:38:33,654 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:33,654 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:33,655 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/smartsdescriptors.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:33,656 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/descriptors/smartsdescriptors.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/descriptors/ -dumpbase smartsdescriptors.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccQNChQZ.s 2025-09-09T00:38:33,668 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:33,669 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:33,669 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:33,670 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:33,671 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:33,671 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:33,671 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:33,671 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:33,672 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:33,672 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:33,672 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:33,672 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:33,673 #include "..." search starts here: 2025-09-09T00:38:33,673 #include <...> search starts here: 2025-09-09T00:38:33,673 /usr/include/eigen3 2025-09-09T00:38:33,673 include 2025-09-09T00:38:33,673 /usr/include/python3.13 2025-09-09T00:38:33,674 /usr/include/c++/14 2025-09-09T00:38:33,674 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:33,674 /usr/include/c++/14/backward 2025-09-09T00:38:33,674 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:33,674 /usr/local/include 2025-09-09T00:38:33,675 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:33,675 /usr/include 2025-09-09T00:38:33,675 End of search list. 2025-09-09T00:38:33,696 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:35,240 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:35,240 from include/openbabel/mol.h:43, 2025-09-09T00:38:35,240 from ./src/descriptors/smartsdescriptors.cpp:21: 2025-09-09T00:38:35,240 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:35,241 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:35,241 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:35,241 | ^ 2025-09-09T00:38:35,241 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:35,241 37 | # define UNUSED(x) x 2025-09-09T00:38:35,241 | ^ 2025-09-09T00:38:35,796 In file included from include/openbabel/mol.h:52: 2025-09-09T00:38:35,797 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:35,797 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:35,797 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:35,797 | ^ 2025-09-09T00:38:35,797 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:35,797 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:35,797 | ^~~~~~~~ 2025-09-09T00:38:35,801 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:35,802 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:35,802 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:35,802 | ^ 2025-09-09T00:38:35,802 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:35,802 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:35,802 | ^~~~~~~~ 2025-09-09T00:38:35,817 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:35,817 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:35,817 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:35,817 | ^ 2025-09-09T00:38:35,817 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:35,818 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:35,818 | ^~~~~~~~ 2025-09-09T00:38:35,823 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:35,823 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:35,823 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:35,823 | ^ 2025-09-09T00:38:35,823 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:35,823 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:35,824 | ^~~~~~~~ 2025-09-09T00:38:36,000 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:38:36,000 from ./src/descriptors/smartsdescriptors.cpp:22: 2025-09-09T00:38:36,000 include/openbabel/plugin.h: At global scope: 2025-09-09T00:38:36,001 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:36,001 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:36,001 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:36,002 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:38:36,002 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:38:36,002 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:38:36,002 from /usr/include/c++/14/ios:44, 2025-09-09T00:38:36,002 from /usr/include/c++/14/istream:40, 2025-09-09T00:38:36,002 from /usr/include/c++/14/sstream:40, 2025-09-09T00:38:36,002 from include/openbabel/oberror.h:26, 2025-09-09T00:38:36,002 from ./src/descriptors/smartsdescriptors.cpp:20: 2025-09-09T00:38:36,002 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:36,002 131 | struct binary_function 2025-09-09T00:38:36,002 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:36,040 ./src/descriptors/smartsdescriptors.cpp: In member function ‘virtual double OpenBabel::SmartsDescriptor::Predict(OpenBabel::OBBase*, std::string*)’: 2025-09-09T00:38:36,040 ./src/descriptors/smartsdescriptors.cpp:48:41: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:38:36,040 48 | double Predict(OBBase* pOb, string* param=NULL) 2025-09-09T00:38:36,040 | ^ 2025-09-09T00:38:37,844 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/smartsdescriptors.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/' 2025-09-09T00:38:37,845 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/descriptors/smartsdescriptors.o /tmp/ccQNChQZ.s 2025-09-09T00:38:37,850 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:37,975 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:37,976 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:37,976 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/descriptors/smartsdescriptors.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/descriptors/smartsdescriptors.' 2025-09-09T00:38:37,978 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/distgeom.cpp -o build/temp.linux-armv7l-cpython-313/src/distgeom.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:37,982 Using built-in specs. 2025-09-09T00:38:37,983 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:37,984 Target: arm-linux-gnueabihf 2025-09-09T00:38:37,984 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:37,984 Thread model: posix 2025-09-09T00:38:37,984 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:37,985 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:37,985 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/distgeom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:37,987 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/distgeom.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase distgeom.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccAyrG4P.s 2025-09-09T00:38:37,998 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:37,998 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:37,999 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:37,999 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:38,000 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:38,000 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:38,000 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:38,000 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:38,000 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:38,001 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:38,001 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:38,001 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:38,001 #include "..." search starts here: 2025-09-09T00:38:38,001 #include <...> search starts here: 2025-09-09T00:38:38,001 /usr/include/eigen3 2025-09-09T00:38:38,002 include 2025-09-09T00:38:38,002 /usr/include/python3.13 2025-09-09T00:38:38,002 /usr/include/c++/14 2025-09-09T00:38:38,002 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:38,002 /usr/include/c++/14/backward 2025-09-09T00:38:38,002 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:38,003 /usr/local/include 2025-09-09T00:38:38,003 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:38,003 /usr/include 2025-09-09T00:38:38,003 End of search list. 2025-09-09T00:38:38,023 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:38,743 ./src/distgeom.cpp:37: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2025-09-09T00:38:38,743 37 | #pragma warning(disable : 4244) // warning C4244: '=' : conversion from 'double' to 'float', possible loss of data 2025-09-09T00:38:38,743 ./src/distgeom.cpp:38: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2025-09-09T00:38:38,743 38 | #pragma warning(disable : 4305) // warning C4305: '*=' : truncation from 'double' to 'float' 2025-09-09T00:38:38,747 ./src/distgeom.cpp:524:3: warning: multi-line comment [-Wcomment] 2025-09-09T00:38:38,747 524 | // \ 2025-09-09T00:38:38,747 | ^ 2025-09-09T00:38:38,750 ./src/distgeom.cpp:881:9: warning: multi-line comment [-Wcomment] 2025-09-09T00:38:38,750 881 | // / \ 2025-09-09T00:38:38,750 | ^ 2025-09-09T00:38:39,807 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:39,807 from include/openbabel/mol.h:43, 2025-09-09T00:38:39,807 from include/openbabel/distgeom.h:24, 2025-09-09T00:38:39,807 from ./src/distgeom.cpp:20: 2025-09-09T00:38:39,808 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:39,808 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:39,808 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:39,808 | ^ 2025-09-09T00:38:39,808 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:39,808 37 | # define UNUSED(x) x 2025-09-09T00:38:39,808 | ^ 2025-09-09T00:38:40,432 In file included from include/openbabel/mol.h:52: 2025-09-09T00:38:40,432 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:40,432 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:40,432 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:40,433 | ^ 2025-09-09T00:38:40,433 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:40,433 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:40,433 | ^~~~~~~~ 2025-09-09T00:38:40,437 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:40,437 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:40,437 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:40,437 | ^ 2025-09-09T00:38:40,438 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:40,438 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:40,438 | ^~~~~~~~ 2025-09-09T00:38:40,452 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:40,453 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:40,453 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:40,453 | ^ 2025-09-09T00:38:40,453 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:40,453 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:40,453 | ^~~~~~~~ 2025-09-09T00:38:40,458 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:40,458 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:40,459 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:40,459 | ^ 2025-09-09T00:38:40,459 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:40,459 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:40,459 | ^~~~~~~~ 2025-09-09T00:38:42,035 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set14Bounds()’: 2025-09-09T00:38:42,035 ./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] 2025-09-09T00:38:42,035 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:38:42,035 ./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] 2025-09-09T00:38:42,035 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:38:42,037 ./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] 2025-09-09T00:38:42,037 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:38:42,037 ./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] 2025-09-09T00:38:42,037 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:38:42,039 ./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] 2025-09-09T00:38:42,039 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:38:42,039 ./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] 2025-09-09T00:38:42,039 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:38:42,040 ./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] 2025-09-09T00:38:42,041 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:38:42,041 ./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] 2025-09-09T00:38:42,041 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:38:42,042 ./src/distgeom.cpp:386:18: warning: unused variable ‘i’ [-Wunused-variable] 2025-09-09T00:38:42,042 386 | unsigned int i, j; 2025-09-09T00:38:42,042 | ^ 2025-09-09T00:38:42,042 ./src/distgeom.cpp:386:21: warning: unused variable ‘j’ [-Wunused-variable] 2025-09-09T00:38:42,043 386 | unsigned int i, j; 2025-09-09T00:38:42,043 | ^ 2025-09-09T00:38:42,043 ./src/distgeom.cpp:426:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2025-09-09T00:38:42,043 426 | OBStereo::Ref bond_id; 2025-09-09T00:38:42,043 | ^~~~~~~ 2025-09-09T00:38:42,050 ./src/distgeom.cpp: In member function ‘OpenBabel::OBCisTransStereo* OpenBabel::OBDistanceGeometry::GetCisTransStereo(OpenBabel::OBBond*)’: 2025-09-09T00:38:42,050 ./src/distgeom.cpp:584:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2025-09-09T00:38:42,050 584 | OBStereo::Ref bond_id; 2025-09-09T00:38:42,050 | ^~~~~~~ 2025-09-09T00:38:42,058 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set15Bounds()’: 2025-09-09T00:38:42,059 ./src/distgeom.cpp:614:18: warning: unused variable ‘i’ [-Wunused-variable] 2025-09-09T00:38:42,059 614 | unsigned int i, j; 2025-09-09T00:38:42,059 | ^ 2025-09-09T00:38:42,059 ./src/distgeom.cpp:614:21: warning: unused variable ‘j’ [-Wunused-variable] 2025-09-09T00:38:42,059 614 | unsigned int i, j; 2025-09-09T00:38:42,059 | ^ 2025-09-09T00:38:42,067 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::TriangleSmooth(int)’: 2025-09-09T00:38:42,067 ./src/distgeom.cpp:745:9: warning: unused variable ‘loopCount’ [-Wunused-variable] 2025-09-09T00:38:42,067 745 | int loopCount = 0; 2025-09-09T00:38:42,068 | ^~~~~~~~~ 2025-09-09T00:38:42,068 ./src/distgeom.cpp:742:47: warning: unused parameter ‘iterations’ [-Wunused-parameter] 2025-09-09T00:38:42,068 742 | void OBDistanceGeometry::TriangleSmooth(int iterations) 2025-09-09T00:38:42,068 | ~~~~^~~~~~~~~~ 2025-09-09T00:38:42,128 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::AddConformer()’: 2025-09-09T00:38:42,128 ./src/distgeom.cpp:1105:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:38:42,128 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2025-09-09T00:38:42,128 | ~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:38:42,128 ./src/distgeom.cpp:1105:52: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:38:42,129 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2025-09-09T00:38:42,129 | ~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:38:42,129 ./src/distgeom.cpp:1105:77: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:38:42,129 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2025-09-09T00:38:42,129 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:38:42,134 ./src/distgeom.cpp:1039:18: warning: unused variable ‘attempts’ [-Wunused-variable] 2025-09-09T00:38:42,134 1039 | unsigned int attempts = 0; 2025-09-09T00:38:42,134 | ^~~~~~~~ 2025-09-09T00:38:52,408 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/distgeom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:52,409 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/distgeom.o /tmp/ccAyrG4P.s 2025-09-09T00:38:52,414 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:53,527 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:53,527 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:53,527 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/distgeom.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/distgeom.' 2025-09-09T00:38:53,532 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/doxygen_pages.cpp -o build/temp.linux-armv7l-cpython-313/src/doxygen_pages.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:53,536 Using built-in specs. 2025-09-09T00:38:53,537 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:53,537 Target: arm-linux-gnueabihf 2025-09-09T00:38:53,537 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:53,538 Thread model: posix 2025-09-09T00:38:53,538 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:53,538 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:53,538 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/doxygen_pages.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:53,540 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/doxygen_pages.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase doxygen_pages.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccWRv3SK.s 2025-09-09T00:38:53,550 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:53,551 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:53,551 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:53,551 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:53,552 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:53,553 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:53,553 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:53,553 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:53,553 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:53,554 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:53,554 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:53,554 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:53,555 #include "..." search starts here: 2025-09-09T00:38:53,555 #include <...> search starts here: 2025-09-09T00:38:53,555 /usr/include/eigen3 2025-09-09T00:38:53,555 include 2025-09-09T00:38:53,555 /usr/include/python3.13 2025-09-09T00:38:53,556 /usr/include/c++/14 2025-09-09T00:38:53,556 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:53,556 /usr/include/c++/14/backward 2025-09-09T00:38:53,556 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:53,556 /usr/local/include 2025-09-09T00:38:53,556 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:53,557 /usr/include 2025-09-09T00:38:53,557 End of search list. 2025-09-09T00:38:53,577 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:53,593 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/doxygen_pages.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:53,594 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/doxygen_pages.o /tmp/ccWRv3SK.s 2025-09-09T00:38:53,599 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:53,602 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:53,603 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:53,603 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/doxygen_pages.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/doxygen_pages.' 2025-09-09T00:38:53,604 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/fingerprint.cpp -o build/temp.linux-armv7l-cpython-313/src/fingerprint.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:53,608 Using built-in specs. 2025-09-09T00:38:53,609 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:53,609 Target: arm-linux-gnueabihf 2025-09-09T00:38:53,610 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:53,610 Thread model: posix 2025-09-09T00:38:53,610 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:53,610 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:53,611 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprint.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:53,612 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprint.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase fingerprint.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cca4HIcP.s 2025-09-09T00:38:53,627 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:53,627 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:53,627 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:53,628 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:53,628 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:53,629 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:53,629 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:53,629 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:53,629 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:53,630 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:53,630 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:53,630 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:53,630 #include "..." search starts here: 2025-09-09T00:38:53,630 #include <...> search starts here: 2025-09-09T00:38:53,631 /usr/include/eigen3 2025-09-09T00:38:53,631 include 2025-09-09T00:38:53,631 /usr/include/python3.13 2025-09-09T00:38:53,631 /usr/include/c++/14 2025-09-09T00:38:53,631 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:53,632 /usr/include/c++/14/backward 2025-09-09T00:38:53,632 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:53,632 /usr/local/include 2025-09-09T00:38:53,632 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:53,632 /usr/include 2025-09-09T00:38:53,633 End of search list. 2025-09-09T00:38:53,649 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:55,067 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:38:55,067 from ./src/fingerprint.cpp:27: 2025-09-09T00:38:55,067 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:55,067 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:55,068 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:55,068 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:38:55,068 from /usr/include/c++/14/vector:68, 2025-09-09T00:38:55,068 from ./src/fingerprint.cpp:21: 2025-09-09T00:38:55,069 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:55,069 131 | struct binary_function 2025-09-09T00:38:55,069 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:55,184 ./src/fingerprint.cpp: In member function ‘bool OpenBabel::FastSearch::Find(OpenBabel::OBBase*, std::vector&, unsigned int)’: 2025-09-09T00:38:55,185 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2025-09-09T00:38:55,185 161 | if ( (a=((*ppat) & (*p++)) ^ (*ppat++)) ) break; 2025-09-09T00:38:55,185 | ~~~~^~ 2025-09-09T00:38:55,185 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2025-09-09T00:38:57,711 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprint.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:38:57,712 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/fingerprint.o /tmp/cca4HIcP.s 2025-09-09T00:38:57,717 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:57,977 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:38:57,977 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:38:57,978 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprint.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprint.' 2025-09-09T00:38:57,980 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/fingerprints/finger2.cpp -o build/temp.linux-armv7l-cpython-313/src/fingerprints/finger2.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:38:57,984 Using built-in specs. 2025-09-09T00:38:57,985 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:57,985 Target: arm-linux-gnueabihf 2025-09-09T00:38:57,986 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:38:57,986 Thread model: posix 2025-09-09T00:38:57,986 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:57,986 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:57,987 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/' 2025-09-09T00:38:57,988 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprints/finger2.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/fingerprints/ -dumpbase finger2.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccrpny7f.s 2025-09-09T00:38:58,002 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:58,003 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:38:58,003 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:58,004 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:58,005 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:58,005 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:58,006 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:58,006 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:58,006 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:58,006 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:58,007 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:58,007 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:58,007 #include "..." search starts here: 2025-09-09T00:38:58,007 #include <...> search starts here: 2025-09-09T00:38:58,008 /usr/include/eigen3 2025-09-09T00:38:58,008 include 2025-09-09T00:38:58,008 /usr/include/python3.13 2025-09-09T00:38:58,008 /usr/include/c++/14 2025-09-09T00:38:58,008 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:58,009 /usr/include/c++/14/backward 2025-09-09T00:38:58,009 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:58,009 /usr/local/include 2025-09-09T00:38:58,009 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:58,009 /usr/include 2025-09-09T00:38:58,010 End of search list. 2025-09-09T00:38:58,029 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:59,516 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:59,516 from include/openbabel/mol.h:43, 2025-09-09T00:38:59,516 from ./src/fingerprints/finger2.cpp:20: 2025-09-09T00:38:59,516 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:59,516 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:59,516 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:59,516 | ^ 2025-09-09T00:38:59,517 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:59,517 37 | # define UNUSED(x) x 2025-09-09T00:38:59,517 | ^ 2025-09-09T00:39:00,128 In file included from include/openbabel/mol.h:52: 2025-09-09T00:39:00,128 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:00,128 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:00,129 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:00,129 | ^ 2025-09-09T00:39:00,129 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:00,129 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:00,129 | ^~~~~~~~ 2025-09-09T00:39:00,133 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:00,133 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:00,133 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:00,133 | ^ 2025-09-09T00:39:00,134 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:00,134 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:00,134 | ^~~~~~~~ 2025-09-09T00:39:00,148 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:00,148 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:00,149 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:00,149 | ^ 2025-09-09T00:39:00,149 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:00,149 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:00,149 | ^~~~~~~~ 2025-09-09T00:39:00,154 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:00,154 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:00,155 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:00,155 | ^ 2025-09-09T00:39:00,155 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:00,155 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:00,155 | ^~~~~~~~ 2025-09-09T00:39:00,310 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:39:00,310 from ./src/fingerprints/finger2.cpp:21: 2025-09-09T00:39:00,310 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:00,310 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:00,310 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:00,310 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:00,311 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:00,311 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:00,311 from include/openbabel/mol.h:35: 2025-09-09T00:39:00,311 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:00,311 131 | struct binary_function 2025-09-09T00:39:00,311 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:00,365 ./src/fingerprints/finger2.cpp: In member function ‘virtual std::string OpenBabel::fingerprint2::DescribeBits(std::vector, bool)’: 2025-09-09T00:39:00,366 ./src/fingerprints/finger2.cpp:63:68: warning: unused parameter ‘fp’ [-Wunused-parameter] 2025-09-09T00:39:00,366 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:39:00,366 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:39:00,366 ./src/fingerprints/finger2.cpp:63:77: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2025-09-09T00:39:00,366 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:39:00,366 | ~~~~~^~~~~~~~~ 2025-09-09T00:39:04,622 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/' 2025-09-09T00:39:04,623 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/fingerprints/finger2.o /tmp/ccrpny7f.s 2025-09-09T00:39:04,628 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:05,018 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:39:05,018 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:39:05,019 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger2.' 2025-09-09T00:39:05,021 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/fingerprints/finger3.cpp -o build/temp.linux-armv7l-cpython-313/src/fingerprints/finger3.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:39:05,025 Using built-in specs. 2025-09-09T00:39:05,027 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:05,027 Target: arm-linux-gnueabihf 2025-09-09T00:39:05,027 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:39:05,027 Thread model: posix 2025-09-09T00:39:05,028 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:05,028 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:05,028 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger3.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/' 2025-09-09T00:39:05,030 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprints/finger3.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/fingerprints/ -dumpbase finger3.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccCTyESZ.s 2025-09-09T00:39:05,040 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:05,041 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:39:05,041 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:05,041 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:05,042 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:05,042 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:05,042 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:05,042 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:05,043 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:05,043 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:05,043 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:05,043 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:05,043 #include "..." search starts here: 2025-09-09T00:39:05,044 #include <...> search starts here: 2025-09-09T00:39:05,044 /usr/include/eigen3 2025-09-09T00:39:05,044 include 2025-09-09T00:39:05,044 /usr/include/python3.13 2025-09-09T00:39:05,044 /usr/include/c++/14 2025-09-09T00:39:05,045 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:05,045 /usr/include/c++/14/backward 2025-09-09T00:39:05,045 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:05,045 /usr/local/include 2025-09-09T00:39:05,045 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:05,045 /usr/include 2025-09-09T00:39:05,046 End of search list. 2025-09-09T00:39:05,067 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:06,559 In file included from include/openbabel/atom.h:33, 2025-09-09T00:39:06,559 from include/openbabel/mol.h:43, 2025-09-09T00:39:06,559 from ./src/fingerprints/finger3.cpp:19: 2025-09-09T00:39:06,559 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:39:06,559 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:39:06,559 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:39:06,560 | ^ 2025-09-09T00:39:06,560 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:06,560 37 | # define UNUSED(x) x 2025-09-09T00:39:06,560 | ^ 2025-09-09T00:39:07,175 In file included from include/openbabel/mol.h:52: 2025-09-09T00:39:07,175 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:07,176 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:07,176 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:07,176 | ^ 2025-09-09T00:39:07,176 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:07,176 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:07,176 | ^~~~~~~~ 2025-09-09T00:39:07,180 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:07,180 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:07,180 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:07,181 | ^ 2025-09-09T00:39:07,181 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:07,181 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:07,181 | ^~~~~~~~ 2025-09-09T00:39:07,195 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:07,196 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:07,196 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:07,196 | ^ 2025-09-09T00:39:07,196 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:07,196 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:07,196 | ^~~~~~~~ 2025-09-09T00:39:07,201 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:07,201 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:07,202 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:07,202 | ^ 2025-09-09T00:39:07,202 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:07,202 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:07,202 | ^~~~~~~~ 2025-09-09T00:39:07,357 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:39:07,357 from ./src/fingerprints/finger3.cpp:26: 2025-09-09T00:39:07,357 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:07,357 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:07,357 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:07,357 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:07,358 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:07,358 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:07,358 from include/openbabel/mol.h:35: 2025-09-09T00:39:07,358 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:07,358 131 | struct binary_function 2025-09-09T00:39:07,358 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:07,411 ./src/fingerprints/finger3.cpp: In member function ‘virtual bool OpenBabel::PatternFP::GetFingerprint(OpenBabel::OBBase*, std::vector&, int)’: 2025-09-09T00:39:07,411 ./src/fingerprints/finger3.cpp:108:13: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:39:07,411 108 | while(n < _bitcount) 2025-09-09T00:39:07,411 | ~~^~~~~~~~~~~ 2025-09-09T00:39:07,427 ./src/fingerprints/finger3.cpp: In member function ‘virtual std::string OpenBabel::PatternFP::DescribeBits(std::vector, bool)’: 2025-09-09T00:39:07,428 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2025-09-09T00:39:07,428 257 | ngrp = (num + div -1)/div--; //rounds up 2025-09-09T00:39:07,428 | ~~~^~ 2025-09-09T00:39:07,428 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2025-09-09T00:39:12,055 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger3.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/' 2025-09-09T00:39:12,057 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/fingerprints/finger3.o /tmp/ccCTyESZ.s 2025-09-09T00:39:12,065 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:12,504 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:39:12,504 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:39:12,505 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger3.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/finger3.' 2025-09-09T00:39:12,507 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/fingerprints/fingerecfp.cpp -o build/temp.linux-armv7l-cpython-313/src/fingerprints/fingerecfp.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:39:12,512 Using built-in specs. 2025-09-09T00:39:12,513 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:12,513 Target: arm-linux-gnueabihf 2025-09-09T00:39:12,513 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:39:12,513 Thread model: posix 2025-09-09T00:39:12,514 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:12,514 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:12,514 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/fingerecfp.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/' 2025-09-09T00:39:12,516 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/fingerprints/fingerecfp.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/fingerprints/ -dumpbase fingerecfp.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc4l0p2c.s 2025-09-09T00:39:12,528 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:12,529 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:39:12,529 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:12,529 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:12,531 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:12,532 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:12,532 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:12,532 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:12,532 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:12,532 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:12,533 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:12,533 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:12,533 #include "..." search starts here: 2025-09-09T00:39:12,533 #include <...> search starts here: 2025-09-09T00:39:12,534 /usr/include/eigen3 2025-09-09T00:39:12,534 include 2025-09-09T00:39:12,534 /usr/include/python3.13 2025-09-09T00:39:12,534 /usr/include/c++/14 2025-09-09T00:39:12,534 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:12,534 /usr/include/c++/14/backward 2025-09-09T00:39:12,535 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:12,535 /usr/local/include 2025-09-09T00:39:12,535 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:12,535 /usr/include 2025-09-09T00:39:12,535 End of search list. 2025-09-09T00:39:12,553 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:14,034 In file included from include/openbabel/atom.h:33, 2025-09-09T00:39:14,034 from include/openbabel/mol.h:43, 2025-09-09T00:39:14,034 from ./src/fingerprints/fingerecfp.cpp:15: 2025-09-09T00:39:14,034 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:39:14,034 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:39:14,034 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:39:14,034 | ^ 2025-09-09T00:39:14,034 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:14,035 37 | # define UNUSED(x) x 2025-09-09T00:39:14,035 | ^ 2025-09-09T00:39:14,645 In file included from include/openbabel/mol.h:52: 2025-09-09T00:39:14,645 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:14,645 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:14,645 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:14,645 | ^ 2025-09-09T00:39:14,646 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:14,646 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:14,646 | ^~~~~~~~ 2025-09-09T00:39:14,650 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:14,650 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:14,650 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:14,650 | ^ 2025-09-09T00:39:14,650 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:14,650 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:14,650 | ^~~~~~~~ 2025-09-09T00:39:14,665 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:14,665 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:14,665 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:14,665 | ^ 2025-09-09T00:39:14,666 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:14,666 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:14,666 | ^~~~~~~~ 2025-09-09T00:39:14,671 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:14,671 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:14,671 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:14,671 | ^ 2025-09-09T00:39:14,671 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:14,671 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:14,672 | ^~~~~~~~ 2025-09-09T00:39:14,825 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:39:14,826 from ./src/fingerprints/fingerecfp.cpp:16: 2025-09-09T00:39:14,826 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:14,826 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:14,826 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:14,826 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:14,827 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:14,827 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:14,827 from include/openbabel/mol.h:35: 2025-09-09T00:39:14,827 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:14,827 131 | struct binary_function 2025-09-09T00:39:14,827 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:14,866 ./src/fingerprints/fingerecfp.cpp: In member function ‘virtual std::string OpenBabel::fingerprintECFP::DescribeBits(std::vector, bool)’: 2025-09-09T00:39:14,866 ./src/fingerprints/fingerecfp.cpp:43:70: warning: unused parameter ‘fp’ [-Wunused-parameter] 2025-09-09T00:39:14,866 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:39:14,866 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:39:14,866 ./src/fingerprints/fingerecfp.cpp:43:79: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2025-09-09T00:39:14,866 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:39:14,866 | ~~~~~^~~~~~~~~ 2025-09-09T00:39:15,875 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(unsigned char*, unsigned int)’: 2025-09-09T00:39:15,875 ./src/fingerprints/fingerecfp.cpp:105:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,875 105 | case 11: c += ((unsigned int)ptr[10]<<24); 2025-09-09T00:39:15,875 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,875 ./src/fingerprints/fingerecfp.cpp:106:3: note: here 2025-09-09T00:39:15,876 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2025-09-09T00:39:15,876 | ^~~~ 2025-09-09T00:39:15,876 ./src/fingerprints/fingerecfp.cpp:106:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,876 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2025-09-09T00:39:15,876 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,876 ./src/fingerprints/fingerecfp.cpp:107:3: note: here 2025-09-09T00:39:15,876 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2025-09-09T00:39:15,876 | ^~~~ 2025-09-09T00:39:15,877 ./src/fingerprints/fingerecfp.cpp:107:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,877 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2025-09-09T00:39:15,877 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,877 ./src/fingerprints/fingerecfp.cpp:108:3: note: here 2025-09-09T00:39:15,877 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2025-09-09T00:39:15,877 | ^~~~ 2025-09-09T00:39:15,877 ./src/fingerprints/fingerecfp.cpp:108:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,877 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2025-09-09T00:39:15,877 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,878 ./src/fingerprints/fingerecfp.cpp:109:3: note: here 2025-09-09T00:39:15,878 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2025-09-09T00:39:15,878 | ^~~~ 2025-09-09T00:39:15,878 ./src/fingerprints/fingerecfp.cpp:109:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,878 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2025-09-09T00:39:15,878 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,878 ./src/fingerprints/fingerecfp.cpp:110:3: note: here 2025-09-09T00:39:15,878 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2025-09-09T00:39:15,878 | ^~~~ 2025-09-09T00:39:15,879 ./src/fingerprints/fingerecfp.cpp:110:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,879 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2025-09-09T00:39:15,879 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,879 ./src/fingerprints/fingerecfp.cpp:111:3: note: here 2025-09-09T00:39:15,879 111 | case 5: b += ptr[4]; 2025-09-09T00:39:15,879 | ^~~~ 2025-09-09T00:39:15,879 ./src/fingerprints/fingerecfp.cpp:111:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,879 111 | case 5: b += ptr[4]; 2025-09-09T00:39:15,880 | ~~^~~~~~~~~ 2025-09-09T00:39:15,880 ./src/fingerprints/fingerecfp.cpp:112:3: note: here 2025-09-09T00:39:15,880 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2025-09-09T00:39:15,880 | ^~~~ 2025-09-09T00:39:15,880 ./src/fingerprints/fingerecfp.cpp:112:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,880 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2025-09-09T00:39:15,880 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,880 ./src/fingerprints/fingerecfp.cpp:113:3: note: here 2025-09-09T00:39:15,880 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2025-09-09T00:39:15,881 | ^~~~ 2025-09-09T00:39:15,881 ./src/fingerprints/fingerecfp.cpp:113:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,881 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2025-09-09T00:39:15,881 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,881 ./src/fingerprints/fingerecfp.cpp:114:3: note: here 2025-09-09T00:39:15,881 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2025-09-09T00:39:15,881 | ^~~~ 2025-09-09T00:39:15,881 ./src/fingerprints/fingerecfp.cpp:114:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,881 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2025-09-09T00:39:15,882 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:15,882 ./src/fingerprints/fingerecfp.cpp:115:3: note: here 2025-09-09T00:39:15,882 115 | case 1: a += ptr[0]; 2025-09-09T00:39:15,882 | ^~~~ 2025-09-09T00:39:15,904 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(std::vector&)’: 2025-09-09T00:39:15,904 ./src/fingerprints/fingerecfp.cpp:139:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:39:15,904 139 | case 2: b += v[i+1]; 2025-09-09T00:39:15,904 ./src/fingerprints/fingerecfp.cpp:140:3: note: here 2025-09-09T00:39:15,905 140 | case 1: a += v[i]; 2025-09-09T00:39:15,905 | ^~~~ 2025-09-09T00:39:18,577 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/fingerecfp.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/' 2025-09-09T00:39:18,578 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/fingerprints/fingerecfp.o /tmp/cc4l0p2c.s 2025-09-09T00:39:18,583 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:18,840 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:39:18,841 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:39:18,841 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/fingerecfp.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/fingerprints/fingerecfp.' 2025-09-09T00:39:18,843 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/forcefield.cpp -o build/temp.linux-armv7l-cpython-313/src/forcefield.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:39:18,847 Using built-in specs. 2025-09-09T00:39:18,848 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:18,848 Target: arm-linux-gnueabihf 2025-09-09T00:39:18,848 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:39:18,849 Thread model: posix 2025-09-09T00:39:18,849 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:18,849 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:18,849 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefield.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:39:18,851 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefield.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase forcefield.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cchcnH0S.s 2025-09-09T00:39:18,862 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:18,863 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:39:18,863 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:18,864 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:18,865 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:18,865 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:18,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:18,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:18,866 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:18,866 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:18,866 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:18,866 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:18,867 #include "..." search starts here: 2025-09-09T00:39:18,867 #include <...> search starts here: 2025-09-09T00:39:18,867 /usr/include/eigen3 2025-09-09T00:39:18,867 include 2025-09-09T00:39:18,867 /usr/include/python3.13 2025-09-09T00:39:18,868 /usr/include/c++/14 2025-09-09T00:39:18,868 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:18,868 /usr/include/c++/14/backward 2025-09-09T00:39:18,868 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:18,868 /usr/local/include 2025-09-09T00:39:18,868 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:18,869 /usr/include 2025-09-09T00:39:18,869 End of search list. 2025-09-09T00:39:18,888 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:20,368 In file included from include/openbabel/forcefield.h:30, 2025-09-09T00:39:20,368 from ./src/forcefield.cpp:22: 2025-09-09T00:39:20,369 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:39:20,369 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:39:20,369 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:39:20,369 | ^ 2025-09-09T00:39:20,369 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:20,369 37 | # define UNUSED(x) x 2025-09-09T00:39:20,369 | ^ 2025-09-09T00:39:21,001 In file included from include/openbabel/mol.h:52, 2025-09-09T00:39:21,001 from include/openbabel/forcefield.h:31: 2025-09-09T00:39:21,001 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:21,001 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:21,001 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:21,001 | ^ 2025-09-09T00:39:21,001 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:21,002 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:21,002 | ^~~~~~~~ 2025-09-09T00:39:21,006 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:21,006 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:21,006 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:21,006 | ^ 2025-09-09T00:39:21,006 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:21,006 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:21,006 | ^~~~~~~~ 2025-09-09T00:39:21,021 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:21,021 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:21,021 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:21,022 | ^ 2025-09-09T00:39:21,022 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:21,022 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:21,022 | ^~~~~~~~ 2025-09-09T00:39:21,027 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:21,027 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:21,027 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:21,027 | ^ 2025-09-09T00:39:21,028 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:21,028 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:21,028 | ^~~~~~~~ 2025-09-09T00:39:21,166 In file included from include/openbabel/forcefield.h:32: 2025-09-09T00:39:21,166 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:21,167 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:21,167 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:21,167 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:21,167 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:21,168 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:21,168 from include/openbabel/forcefield.h:23: 2025-09-09T00:39:21,168 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:21,168 131 | struct binary_function 2025-09-09T00:39:21,168 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:21,203 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:39:21,203 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:39:21,203 55 | virtual void Init(OBMol &box); 2025-09-09T00:39:21,203 | ^~~~ 2025-09-09T00:39:21,203 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:39:21,203 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:39:21,203 | ^~~~ 2025-09-09T00:39:21,215 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:39:21,215 229 | virtual const std::string &GetValue() const 2025-09-09T00:39:21,215 | ^~~~~~~~ 2025-09-09T00:39:21,215 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:39:21,216 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:39:21,216 76 | double GetValue (vector3 pos) const; 2025-09-09T00:39:21,216 | ^~~~~~~~ 2025-09-09T00:39:21,273 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:39:21,273 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,273 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,273 | ^ 2025-09-09T00:39:21,273 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,273 37 | # define UNUSED(x) x 2025-09-09T00:39:21,273 | ^ 2025-09-09T00:39:21,274 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:39:21,274 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,274 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,274 | ^ 2025-09-09T00:39:21,274 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,274 37 | # define UNUSED(x) x 2025-09-09T00:39:21,274 | ^ 2025-09-09T00:39:21,275 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:39:21,275 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,275 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,275 | ^ 2025-09-09T00:39:21,275 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,275 37 | # define UNUSED(x) x 2025-09-09T00:39:21,275 | ^ 2025-09-09T00:39:21,276 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:39:21,276 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,276 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,276 | ^ 2025-09-09T00:39:21,276 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,276 37 | # define UNUSED(x) x 2025-09-09T00:39:21,276 | ^ 2025-09-09T00:39:21,277 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:39:21,277 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,277 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,277 | ^ 2025-09-09T00:39:21,277 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,277 37 | # define UNUSED(x) x 2025-09-09T00:39:21,277 | ^ 2025-09-09T00:39:21,277 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:39:21,278 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,278 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,278 | ^ 2025-09-09T00:39:21,278 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,278 37 | # define UNUSED(x) x 2025-09-09T00:39:21,278 | ^ 2025-09-09T00:39:21,278 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:39:21,279 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,279 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,279 | ^ 2025-09-09T00:39:21,279 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,279 37 | # define UNUSED(x) x 2025-09-09T00:39:21,279 | ^ 2025-09-09T00:39:21,279 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:39:21,279 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:21,280 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:21,280 | ^ 2025-09-09T00:39:21,280 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,280 37 | # define UNUSED(x) x 2025-09-09T00:39:21,280 | ^ 2025-09-09T00:39:21,314 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:39:21,314 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:39:21,314 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:39:21,315 | ^ 2025-09-09T00:39:21,315 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,315 37 | # define UNUSED(x) x 2025-09-09T00:39:21,315 | ^ 2025-09-09T00:39:21,316 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:39:21,316 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:39:21,316 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:39:21,316 | ^ 2025-09-09T00:39:21,316 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:21,316 37 | # define UNUSED(x) x 2025-09-09T00:39:21,316 | ^ 2025-09-09T00:39:21,408 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int)’: 2025-09-09T00:39:21,408 ./src/forcefield.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:39:21,408 384 | if (_ignoreAtom == a) 2025-09-09T00:39:21,408 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:39:21,409 ./src/forcefield.cpp:386:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:39:21,409 386 | if (_ignoreAtom == b) 2025-09-09T00:39:21,409 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:39:21,410 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int)’: 2025-09-09T00:39:21,410 ./src/forcefield.cpp:396:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:39:21,410 396 | if (_ignoreAtom == b) 2025-09-09T00:39:21,410 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:39:21,411 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int, int)’: 2025-09-09T00:39:21,411 ./src/forcefield.cpp:406:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:39:21,411 406 | if (_ignoreAtom == d) 2025-09-09T00:39:21,411 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:39:21,431 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintType(int) const’: 2025-09-09T00:39:21,431 ./src/forcefield.cpp:658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,431 658 | if (index >= _constraints.size()) 2025-09-09T00:39:21,431 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:21,432 ./src/forcefield.cpp: In member function ‘double OpenBabel::OBFFConstraints::GetConstraintValue(int) const’: 2025-09-09T00:39:21,432 ./src/forcefield.cpp:666:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,432 666 | if (index >= _constraints.size()) 2025-09-09T00:39:21,432 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:21,433 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomA(int) const’: 2025-09-09T00:39:21,433 ./src/forcefield.cpp:674:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,433 674 | if (index >= _constraints.size()) 2025-09-09T00:39:21,433 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:21,434 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomB(int) const’: 2025-09-09T00:39:21,434 ./src/forcefield.cpp:682:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,434 682 | if (index >= _constraints.size()) 2025-09-09T00:39:21,434 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:21,435 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomC(int) const’: 2025-09-09T00:39:21,435 ./src/forcefield.cpp:690:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,435 690 | if (index >= _constraints.size()) 2025-09-09T00:39:21,435 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:21,436 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomD(int) const’: 2025-09-09T00:39:21,436 ./src/forcefield.cpp:698:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,436 698 | if (index >= _constraints.size()) 2025-09-09T00:39:21,436 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:21,485 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2025-09-09T00:39:21,485 ./src/forcefield.cpp:1358:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-09T00:39:21,486 1358 | num_permutations = factorial[num_rotors_to_permute]; 2025-09-09T00:39:21,486 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:21,487 ./src/forcefield.cpp:1362:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,487 1362 | for (int i=0; i::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:39:21,504 1375 | for (int i=0; i >&, std::vector, double)’: 2025-09-09T00:39:21,530 ./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] 2025-09-09T00:39:21,530 1576 | if (j == rotorKey[i]) 2025-09-09T00:39:21,531 ./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] 2025-09-09T00:39:21,532 1595 | if (j == rotorKey[i]) 2025-09-09T00:39:21,553 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::DistanceGeometry()’: 2025-09-09T00:39:21,553 ./src/forcefield.cpp:1975:26: warning: variable ‘l_bc’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:39:21,553 1975 | double l_ab, l_bc, l_ac; // lower limits 2025-09-09T00:39:21,553 | ^~~~ 2025-09-09T00:39:21,595 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::SteepestDescentInitialize(int, double, int)’: 2025-09-09T00:39:21,596 ./src/forcefield.cpp:2747:77: warning: unused parameter ‘method’ [-Wunused-parameter] 2025-09-09T00:39:21,596 2747 | void OBForceField::SteepestDescentInitialize(int steps, double econv, int method) 2025-09-09T00:39:21,596 | ~~~~^~~~~~ 2025-09-09T00:39:21,605 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ConjugateGradientsInitialize(int, double, int)’: 2025-09-09T00:39:21,605 ./src/forcefield.cpp:2873:55: warning: unused parameter ‘method’ [-Wunused-parameter] 2025-09-09T00:39:21,605 2873 | int method) 2025-09-09T00:39:21,605 | ~~~~^~~~~~ 2025-09-09T00:39:21,638 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::MolecularDynamicsTakeNSteps(int, double, double, int)’: 2025-09-09T00:39:21,638 ./src/forcefield.cpp:3524:88: warning: unused parameter ‘method’ [-Wunused-parameter] 2025-09-09T00:39:21,639 3524 | void OBForceField::MolecularDynamicsTakeNSteps(int n, double T, double timestep, int method) 2025-09-09T00:39:21,639 | ~~~~^~~~~~ 2025-09-09T00:39:28,680 In member function ‘void OpenBabel::OBForceField::PrintTypes()’, 2025-09-09T00:39:28,680 inlined from ‘void OpenBabel::OBForceField::PrintTypes()’ at ./src/forcefield.cpp:735:8: 2025-09-09T00:39:28,680 ./src/forcefield.cpp:742:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:28,681 742 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:39:28,681 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:28,681 743 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:39:28,681 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:28,731 In member function ‘void OpenBabel::OBForceField::PrintFormalCharges()’, 2025-09-09T00:39:28,731 inlined from ‘void OpenBabel::OBForceField::PrintFormalCharges()’ at ./src/forcefield.cpp:749:8: 2025-09-09T00:39:28,731 ./src/forcefield.cpp:756:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:28,731 756 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:39:28,731 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:28,772 In member function ‘void OpenBabel::OBForceField::PrintPartialCharges()’, 2025-09-09T00:39:28,772 inlined from ‘void OpenBabel::OBForceField::PrintPartialCharges()’ at ./src/forcefield.cpp:762:8: 2025-09-09T00:39:28,772 ./src/forcefield.cpp:769:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:28,772 769 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:39:28,772 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:28,814 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::PrintVelocities()’: 2025-09-09T00:39:28,814 ./src/forcefield.cpp:782:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:28,814 782 | snprintf(_logbuf, BUFF_SIZE, "%d\t<%8.3f, %8.3f, %8.3f>\n", a->GetIdx(), _velocityPtr[a->GetIdx()], 2025-09-09T00:39:28,815 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:28,815 783 | _velocityPtr[a->GetIdx()+1], _velocityPtr[a->GetIdx()+2]); 2025-09-09T00:39:28,815 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,498 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ValidateSteepestDescent(int)’: 2025-09-09T00:39:29,498 ./src/forcefield.cpp:2662:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:29,498 2662 | snprintf(_logbuf, BUFF_SIZE, " %4d %8.3f %8.3f\n", i, e_n2, e_n1); 2025-09-09T00:39:29,499 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,665 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ValidateConjugateGradients(int)’: 2025-09-09T00:39:29,665 ./src/forcefield.cpp:2710:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:29,665 2710 | snprintf(_logbuf, BUFF_SIZE, " %4d %8.3f %8.3f\n", i, e_n2, e_n1); 2025-09-09T00:39:29,665 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,666 ./src/forcefield.cpp:2730:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:29,666 2730 | snprintf(_logbuf, BUFF_SIZE, " %4d %8.3f %8.3f\n", i, e_n2, e_n1); 2025-09-09T00:39:29,666 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,033 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2025-09-09T00:39:33,034 ./src/forcefield.cpp:1398:29: warning: ‘minj’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,034 1398 | rotorKey[idx + 1] = minj; 2025-09-09T00:39:33,034 | ^~~~ 2025-09-09T00:39:33,034 ./src/forcefield.cpp:1324:21: note: ‘minj’ was declared here 2025-09-09T00:39:33,034 1324 | unsigned int j, minj; 2025-09-09T00:39:33,034 | ^~~~ 2025-09-09T00:39:33,035 ./src/forcefield.cpp:1415:11: warning: ‘minE’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,035 1415 | if (minE < best_minE) { 2025-09-09T00:39:33,035 | ^~ 2025-09-09T00:39:33,035 ./src/forcefield.cpp:1325:22: note: ‘minE’ was declared here 2025-09-09T00:39:33,035 1325 | double currentE, minE, best_minE; 2025-09-09T00:39:33,035 | ^~~~ 2025-09-09T00:39:34,143 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::DistanceGeometry()’: 2025-09-09T00:39:34,143 ./src/forcefield.cpp:1948:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:34,143 1948 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", matrix[i][j]); 2025-09-09T00:39:34,143 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:34,144 ./src/forcefield.cpp:2030:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:34,144 2030 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", matrix[i][j]); 2025-09-09T00:39:34,144 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:34,144 ./src/forcefield.cpp:2073:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:34,144 2073 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", matrix[i][j]); 2025-09-09T00:39:34,144 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:34,145 ./src/forcefield.cpp:2095:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:34,145 2095 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", G[i][j]); 2025-09-09T00:39:34,145 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:34,146 ./src/forcefield.cpp:2118:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:34,146 2118 | snprintf(_logbuf, BUFF_SIZE, "%8.4f ", eigenvalues[i]); 2025-09-09T00:39:34,146 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:34,146 ./src/forcefield.cpp:2127:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:34,146 2127 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", eigenvectors[i][j]); 2025-09-09T00:39:34,146 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:36,755 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,755 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,755 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,756 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,756 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2025-09-09T00:39:36,756 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,756 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,756 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,756 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2025-09-09T00:39:36,756 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,756 645 | OBFFConstraint constraint; 2025-09-09T00:39:36,756 | ^~~~~~~~~~ 2025-09-09T00:39:36,757 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,757 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,757 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,757 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,757 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2025-09-09T00:39:36,757 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,757 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,758 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,758 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2025-09-09T00:39:36,758 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,758 645 | OBFFConstraint constraint; 2025-09-09T00:39:36,758 | ^~~~~~~~~~ 2025-09-09T00:39:36,802 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,803 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,803 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,803 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,803 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2025-09-09T00:39:36,803 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,803 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,803 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,803 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2025-09-09T00:39:36,804 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,804 570 | OBFFConstraint constraint; 2025-09-09T00:39:36,804 | ^~~~~~~~~~ 2025-09-09T00:39:36,804 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,804 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,804 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,804 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,805 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2025-09-09T00:39:36,805 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,805 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,805 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,805 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2025-09-09T00:39:36,805 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,805 570 | OBFFConstraint constraint; 2025-09-09T00:39:36,805 | ^~~~~~~~~~ 2025-09-09T00:39:36,849 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,849 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,849 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,849 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,850 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2025-09-09T00:39:36,850 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,850 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,850 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,850 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2025-09-09T00:39:36,850 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,850 580 | OBFFConstraint constraint; 2025-09-09T00:39:36,850 | ^~~~~~~~~~ 2025-09-09T00:39:36,850 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,851 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,851 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,851 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,851 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2025-09-09T00:39:36,851 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,851 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,851 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,851 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2025-09-09T00:39:36,851 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,851 580 | OBFFConstraint constraint; 2025-09-09T00:39:36,852 | ^~~~~~~~~~ 2025-09-09T00:39:36,898 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,899 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,899 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,899 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,899 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2025-09-09T00:39:36,899 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,899 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,899 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,899 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2025-09-09T00:39:36,900 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,900 591 | OBFFConstraint constraint; 2025-09-09T00:39:36,900 | ^~~~~~~~~~ 2025-09-09T00:39:36,900 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,900 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,900 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,900 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,901 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2025-09-09T00:39:36,901 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,901 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,901 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,901 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2025-09-09T00:39:36,901 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,901 591 | OBFFConstraint constraint; 2025-09-09T00:39:36,901 | ^~~~~~~~~~ 2025-09-09T00:39:36,944 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,944 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,945 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,945 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,945 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2025-09-09T00:39:36,945 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,945 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,945 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,945 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2025-09-09T00:39:36,945 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,945 602 | OBFFConstraint constraint; 2025-09-09T00:39:36,946 | ^~~~~~~~~~ 2025-09-09T00:39:36,946 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,946 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,946 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,946 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,946 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2025-09-09T00:39:36,946 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,947 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,947 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,947 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2025-09-09T00:39:36,947 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,947 602 | OBFFConstraint constraint; 2025-09-09T00:39:36,947 | ^~~~~~~~~~ 2025-09-09T00:39:36,990 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,991 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,991 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFConstraint; _Args = {const OpenBabel::OBFFConstraint&}; _Tp = OpenBabel::OBFFConstraint]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,991 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,991 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2025-09-09T00:39:36,991 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,991 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,991 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,991 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2025-09-09T00:39:36,992 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,992 613 | OBFFConstraint constraint; 2025-09-09T00:39:36,992 | ^~~~~~~~~~ 2025-09-09T00:39:36,992 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:36,992 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:36,992 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:36,992 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:36,992 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2025-09-09T00:39:36,993 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:36,993 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:36,993 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:36,993 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2025-09-09T00:39:36,993 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2025-09-09T00:39:36,993 613 | OBFFConstraint constraint; 2025-09-09T00:39:36,993 | ^~~~~~~~~~ 2025-09-09T00:39:37,036 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:37,036 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:37,036 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:37,036 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:37,037 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2025-09-09T00:39:37,037 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:37,037 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:37,037 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:37,037 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2025-09-09T00:39:37,037 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2025-09-09T00:39:37,037 622 | OBFFConstraint constraint; 2025-09-09T00:39:37,037 | ^~~~~~~~~~ 2025-09-09T00:39:37,038 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:37,038 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:37,038 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:37,038 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:37,038 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2025-09-09T00:39:37,038 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:37,038 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:37,038 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:37,039 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2025-09-09T00:39:37,039 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2025-09-09T00:39:37,039 622 | OBFFConstraint constraint; 2025-09-09T00:39:37,039 | ^~~~~~~~~~ 2025-09-09T00:39:37,081 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:37,082 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:37,082 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:37,082 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:37,082 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2025-09-09T00:39:37,082 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:37,082 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:37,082 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:37,083 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2025-09-09T00:39:37,083 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2025-09-09T00:39:37,083 633 | OBFFConstraint constraint; 2025-09-09T00:39:37,083 | ^~~~~~~~~~ 2025-09-09T00:39:37,083 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:39:37,083 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:37,083 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:37,083 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFConstraint; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:37,084 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2025-09-09T00:39:37,084 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:37,084 235 | class OBFPRT OBFFConstraint 2025-09-09T00:39:37,084 | ^~~~~~~~~~~~~~ 2025-09-09T00:39:37,084 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2025-09-09T00:39:37,084 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2025-09-09T00:39:37,084 633 | OBFFConstraint constraint; 2025-09-09T00:39:37,084 | ^~~~~~~~~~ 2025-09-09T00:39:38,111 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’: 2025-09-09T00:39:38,111 ./src/forcefield.cpp:1830:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:38,111 1830 | snprintf(_logbuf, BUFF_SIZE, " Weight: %d", i); 2025-09-09T00:39:38,112 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:38,112 ./src/forcefield.cpp:1833:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:38,112 1833 | snprintf(_logbuf, BUFF_SIZE, " %8.3f", rotorWeights[i][j]); 2025-09-09T00:39:38,112 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:41,392 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefield.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:39:41,392 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/forcefield.o /tmp/cchcnH0S.s 2025-09-09T00:39:41,397 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:42,947 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:39:42,947 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:39:42,947 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefield.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefield.' 2025-09-09T00:39:42,947 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/forcefields/forcefieldgaff.cpp -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldgaff.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:39:42,951 Using built-in specs. 2025-09-09T00:39:42,953 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:42,953 Target: arm-linux-gnueabihf 2025-09-09T00:39:42,954 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:39:42,954 Thread model: posix 2025-09-09T00:39:42,954 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:42,954 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:42,955 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldgaff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:39:42,957 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldgaff.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/forcefields/ -dumpbase forcefieldgaff.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccdY760C.s 2025-09-09T00:39:42,970 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:42,970 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:39:42,970 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:42,971 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:42,971 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:42,972 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:42,972 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:42,972 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:42,972 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:42,972 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:42,973 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:42,973 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:42,973 #include "..." search starts here: 2025-09-09T00:39:42,973 #include <...> search starts here: 2025-09-09T00:39:42,973 /usr/include/eigen3 2025-09-09T00:39:42,974 include 2025-09-09T00:39:42,974 /usr/include/python3.13 2025-09-09T00:39:42,974 /usr/include/c++/14 2025-09-09T00:39:42,974 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:42,974 /usr/include/c++/14/backward 2025-09-09T00:39:42,974 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:42,975 /usr/local/include 2025-09-09T00:39:42,975 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:42,975 /usr/include 2025-09-09T00:39:42,975 End of search list. 2025-09-09T00:39:42,994 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:44,485 In file included from include/openbabel/atom.h:33, 2025-09-09T00:39:44,485 from include/openbabel/mol.h:43, 2025-09-09T00:39:44,485 from ./src/forcefields/forcefieldgaff.cpp:21: 2025-09-09T00:39:44,485 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:39:44,485 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:39:44,485 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:39:44,485 | ^ 2025-09-09T00:39:44,486 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:44,486 37 | # define UNUSED(x) x 2025-09-09T00:39:44,486 | ^ 2025-09-09T00:39:45,096 In file included from include/openbabel/mol.h:52: 2025-09-09T00:39:45,096 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:45,096 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:45,096 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:45,097 | ^ 2025-09-09T00:39:45,097 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:45,097 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:45,097 | ^~~~~~~~ 2025-09-09T00:39:45,101 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:45,101 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:45,101 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:45,101 | ^ 2025-09-09T00:39:45,102 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:45,102 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:45,102 | ^~~~~~~~ 2025-09-09T00:39:45,116 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:45,116 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:45,117 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:45,117 | ^ 2025-09-09T00:39:45,117 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:45,117 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:45,117 | ^~~~~~~~ 2025-09-09T00:39:45,122 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:45,122 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:45,122 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:45,122 | ^ 2025-09-09T00:39:45,123 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:45,123 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:45,123 | ^~~~~~~~ 2025-09-09T00:39:45,401 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:39:45,401 from include/forcefields/forcefieldgaff.h:24, 2025-09-09T00:39:45,401 from ./src/forcefields/forcefieldgaff.cpp:24: 2025-09-09T00:39:45,401 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:45,401 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:45,401 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:45,401 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:45,402 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:45,402 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:45,402 from include/openbabel/mol.h:35: 2025-09-09T00:39:45,402 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:45,402 131 | struct binary_function 2025-09-09T00:39:45,402 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:45,437 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:39:45,438 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:39:45,438 55 | virtual void Init(OBMol &box); 2025-09-09T00:39:45,438 | ^~~~ 2025-09-09T00:39:45,438 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:39:45,438 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:39:45,438 | ^~~~ 2025-09-09T00:39:45,449 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:39:45,450 229 | virtual const std::string &GetValue() const 2025-09-09T00:39:45,450 | ^~~~~~~~ 2025-09-09T00:39:45,450 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:39:45,450 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:39:45,450 76 | double GetValue (vector3 pos) const; 2025-09-09T00:39:45,450 | ^~~~~~~~ 2025-09-09T00:39:45,509 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:39:45,509 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,509 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,509 | ^ 2025-09-09T00:39:45,509 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,509 37 | # define UNUSED(x) x 2025-09-09T00:39:45,509 | ^ 2025-09-09T00:39:45,510 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:39:45,510 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,510 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,510 | ^ 2025-09-09T00:39:45,510 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,510 37 | # define UNUSED(x) x 2025-09-09T00:39:45,510 | ^ 2025-09-09T00:39:45,511 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:39:45,511 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,511 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,511 | ^ 2025-09-09T00:39:45,511 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,511 37 | # define UNUSED(x) x 2025-09-09T00:39:45,511 | ^ 2025-09-09T00:39:45,512 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:39:45,512 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,512 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,512 | ^ 2025-09-09T00:39:45,512 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,512 37 | # define UNUSED(x) x 2025-09-09T00:39:45,512 | ^ 2025-09-09T00:39:45,513 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:39:45,513 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,513 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,513 | ^ 2025-09-09T00:39:45,513 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,513 37 | # define UNUSED(x) x 2025-09-09T00:39:45,513 | ^ 2025-09-09T00:39:45,514 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:39:45,514 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,514 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,514 | ^ 2025-09-09T00:39:45,514 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,514 37 | # define UNUSED(x) x 2025-09-09T00:39:45,514 | ^ 2025-09-09T00:39:45,514 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:39:45,515 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,515 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,515 | ^ 2025-09-09T00:39:45,515 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,515 37 | # define UNUSED(x) x 2025-09-09T00:39:45,515 | ^ 2025-09-09T00:39:45,515 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:39:45,515 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:45,516 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:45,516 | ^ 2025-09-09T00:39:45,516 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:45,516 37 | # define UNUSED(x) x 2025-09-09T00:39:45,516 | ^ 2025-09-09T00:39:51,091 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Bond() [with bool = true]’: 2025-09-09T00:39:51,092 ./src/forcefields/forcefieldgaff.cpp:82:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:51,092 82 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:51,092 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,092 83 | (*i).rab, (*i).r0, (*i).kr, (*i).delta, (*i).energy); 2025-09-09T00:39:51,092 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,244 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Bond() [with bool = false]’: 2025-09-09T00:39:51,244 ./src/forcefields/forcefieldgaff.cpp:82:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:51,244 82 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:51,244 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,244 83 | (*i).rab, (*i).r0, (*i).kr, (*i).delta, (*i).energy); 2025-09-09T00:39:51,245 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,394 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Angle() [with bool = true]’: 2025-09-09T00:39:51,394 ./src/forcefields/forcefieldgaff.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:51,394 152 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:51,394 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,394 153 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).kth, (*i).delta, (*i).energy); 2025-09-09T00:39:51,394 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,573 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Angle() [with bool = false]’: 2025-09-09T00:39:51,574 ./src/forcefields/forcefieldgaff.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:51,574 152 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:51,574 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,574 153 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).kth, (*i).delta, (*i).energy); 2025-09-09T00:39:51,574 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,698 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Torsion() [with bool = false]’: 2025-09-09T00:39:51,698 ./src/forcefields/forcefieldgaff.cpp:225:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:51,698 225 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %s %6.3f %5.0f %8.3f %1.0f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:51,698 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,699 226 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:39:51,699 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,828 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_OOP() [with bool = false]’: 2025-09-09T00:39:51,828 ./src/forcefields/forcefieldgaff.cpp:327:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:51,828 327 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %s %6.3f %5.0f %8.3f %1.0f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:51,828 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,828 328 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:39:51,828 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,966 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_VDW() [with bool = false]’: 2025-09-09T00:39:51,966 ./src/forcefields/forcefieldgaff.cpp:402:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:51,966 402 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:51,966 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:51,967 403 | (*i).rab, (*i).energy); 2025-09-09T00:39:51,967 | ~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:52,253 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Electrostatic() [with bool = false]’: 2025-09-09T00:39:52,253 ./src/forcefields/forcefieldgaff.cpp:470:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:52,254 470 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:52,254 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:52,254 471 | (*i).rab, (*i).qq, (*i).energy); 2025-09-09T00:39:52,254 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:52,623 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Torsion() [with bool = true]’: 2025-09-09T00:39:52,623 ./src/forcefields/forcefieldgaff.cpp:225:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:52,623 225 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %s %6.3f %5.0f %8.3f %1.0f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:52,624 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:52,624 226 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:39:52,624 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:52,843 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_OOP() [with bool = true]’: 2025-09-09T00:39:52,843 ./src/forcefields/forcefieldgaff.cpp:327:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:52,843 327 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %s %6.3f %5.0f %8.3f %1.0f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:52,843 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:52,844 328 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:39:52,844 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,043 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,043 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:39:55,043 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,044 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,044 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,044 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2025-09-09T00:39:55,044 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,044 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,044 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,044 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,044 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:39:55,045 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:39:55,045 | ^~~~~~~~ 2025-09-09T00:39:55,045 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,045 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:39:55,045 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,045 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,046 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,046 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2025-09-09T00:39:55,046 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,046 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,046 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,046 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,046 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:39:55,046 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:39:55,046 | ^~~~~~~~ 2025-09-09T00:39:55,047 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,047 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:39:55,047 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,047 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,047 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,047 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2025-09-09T00:39:55,048 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,048 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,048 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,048 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,048 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:39:55,048 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:39:55,048 | ^~~~~~~~ 2025-09-09T00:39:55,049 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,049 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:39:55,049 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,049 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,049 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,049 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2025-09-09T00:39:55,049 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,049 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,050 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,050 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,050 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:39:55,050 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:39:55,050 | ^~~~~~~~ 2025-09-09T00:39:55,051 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,051 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,051 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:39:55,051 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,051 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,051 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,051 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2025-09-09T00:39:55,052 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,052 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,052 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,052 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,052 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:39:55,052 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:39:55,052 | ^~~~~~~~~ 2025-09-09T00:39:55,053 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,053 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,053 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:39:55,053 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,053 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,053 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,053 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2025-09-09T00:39:55,054 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,054 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,054 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,060 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,060 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:39:55,060 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:39:55,060 | ^~~~~~~~~ 2025-09-09T00:39:55,060 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:55,060 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:39:55,060 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,060 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,061 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,061 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2025-09-09T00:39:55,061 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,061 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:55,061 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,061 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,061 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:39:55,061 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:39:55,061 | ^~~~~~~~~ 2025-09-09T00:39:55,062 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,062 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,062 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:39:55,062 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,062 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,062 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,062 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2025-09-09T00:39:55,062 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,063 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,063 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,063 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,063 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:39:55,063 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:39:55,063 | ^~~~~~~~~ 2025-09-09T00:39:55,063 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,063 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,064 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:39:55,064 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,064 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,064 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,064 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2025-09-09T00:39:55,064 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,064 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,065 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,065 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,065 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:39:55,065 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:39:55,065 | ^~~~~~~~~ 2025-09-09T00:39:55,065 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:55,065 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:39:55,065 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,066 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,066 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,066 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2025-09-09T00:39:55,066 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,066 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:55,066 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,066 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,066 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:39:55,067 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:39:55,067 | ^~~~~~~~~ 2025-09-09T00:39:55,067 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,067 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,067 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,067 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,067 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,068 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,068 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,068 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:39:55,068 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,068 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,068 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,068 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,069 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,069 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,069 | ^~~~~~~~~~~ 2025-09-09T00:39:55,069 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,069 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,069 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,069 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,069 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,070 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,070 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,070 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:39:55,070 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,070 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,070 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,070 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,071 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,071 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,071 | ^~~~~~~~~~~ 2025-09-09T00:39:55,071 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:55,071 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,071 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,071 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,071 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,072 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,072 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:39:55,072 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,072 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:55,072 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,072 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,072 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,072 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,073 | ^~~~~~~~~~~ 2025-09-09T00:39:55,073 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:39:55,073 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,073 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,073 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,073 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,073 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:39:55,074 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,074 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:39:55,074 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,074 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,074 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,074 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,074 | ^~~~~~~~~~~ 2025-09-09T00:39:55,075 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,075 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,075 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,075 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,075 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,075 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,075 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,075 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:39:55,076 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,076 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,076 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,076 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,076 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,076 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,076 | ^~~~~~~~~~~ 2025-09-09T00:39:55,077 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,077 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,077 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,077 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,077 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,077 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,077 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,078 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:39:55,078 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,078 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,078 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,078 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,078 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,078 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,079 | ^~~~~~~~~~~ 2025-09-09T00:39:55,079 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:55,079 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,079 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,079 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,079 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,079 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,080 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:39:55,080 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,080 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:55,080 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,080 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,080 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,081 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,081 | ^~~~~~~~~~~ 2025-09-09T00:39:55,081 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:39:55,081 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:39:55,081 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,081 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,081 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,082 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:39:55,082 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,082 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:39:55,082 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,082 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,082 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:39:55,082 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:39:55,082 | ^~~~~~~~~~~ 2025-09-09T00:39:55,082 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,083 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,083 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,083 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,083 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,083 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,083 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,083 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:39:55,083 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,083 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,083 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,084 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,084 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,084 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,084 | ^~~~~~~ 2025-09-09T00:39:55,084 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,084 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,084 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,084 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,085 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,085 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,085 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,085 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:39:55,085 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,085 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,085 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,085 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,085 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,085 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,086 | ^~~~~~~ 2025-09-09T00:39:55,086 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:55,086 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,086 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,086 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,086 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,086 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,086 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:39:55,086 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,087 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:55,087 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,087 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,087 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,087 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,087 | ^~~~~~~ 2025-09-09T00:39:55,087 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:39:55,087 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,087 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,088 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,088 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,088 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:39:55,088 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,088 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:39:55,088 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,088 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,089 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,089 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,089 | ^~~~~~~ 2025-09-09T00:39:55,089 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,089 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,089 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,089 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,089 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,089 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,090 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,090 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:39:55,090 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,090 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,090 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,090 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,090 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,090 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,090 | ^~~~~~~ 2025-09-09T00:39:55,090 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,091 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:55,091 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,091 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,091 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,091 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,091 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,091 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:39:55,091 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,091 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,092 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,092 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,092 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,092 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,092 | ^~~~~~~ 2025-09-09T00:39:55,092 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:55,092 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:55,092 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,092 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,092 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,093 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,093 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:39:55,093 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,093 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:55,093 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,093 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,093 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,093 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,093 | ^~~~~~~ 2025-09-09T00:39:55,093 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:39:55,094 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:39:55,094 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,094 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,094 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFOOPCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,094 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:39:55,094 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,095 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:39:55,095 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,095 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,095 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:39:55,095 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:39:55,095 | ^~~~~~~ 2025-09-09T00:39:55,095 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,095 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:63:9, 2025-09-09T00:39:55,096 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,096 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,096 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,096 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:39:55,096 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,096 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,096 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,096 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,096 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:55,097 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:39:55,097 | ^~~~~~~ 2025-09-09T00:39:55,097 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’, 2025-09-09T00:39:55,097 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,097 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,097 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,097 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:39:55,097 include/forcefields/forcefieldgaff.h:63:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::is14))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,097 63 | class OBFFVDWCalculationGaff : public OBFFCalculation2 2025-09-09T00:39:55,098 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,098 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,098 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::is14))’ was declared here 2025-09-09T00:39:55,098 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:39:55,098 | ^~~~~~~ 2025-09-09T00:39:55,098 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’, 2025-09-09T00:39:55,098 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,098 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,099 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,099 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:39:55,099 include/forcefields/forcefieldgaff.h:63:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::samering))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,099 63 | class OBFFVDWCalculationGaff : public OBFFCalculation2 2025-09-09T00:39:55,099 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,099 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,099 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::samering))’ was declared here 2025-09-09T00:39:55,099 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:39:55,099 | ^~~~~~~ 2025-09-09T00:39:55,099 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’, 2025-09-09T00:39:55,100 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,100 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationGaff; _Args = {const OpenBabel::OBFFVDWCalculationGaff&}; _Tp = OpenBabel::OBFFVDWCalculationGaff]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,100 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,100 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:39:55,100 include/forcefields/forcefieldgaff.h:63:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,100 63 | class OBFFVDWCalculationGaff : public OBFFCalculation2 2025-09-09T00:39:55,100 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,100 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,101 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::rab’ was declared here 2025-09-09T00:39:55,101 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:39:55,101 | ^~~~~~~ 2025-09-09T00:39:55,101 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:55,101 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGaff::OBFFElectrostaticCalculationGaff(const OpenBabel::OBFFElectrostaticCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:72:9, 2025-09-09T00:39:55,101 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGaff; _Args = {const OpenBabel::OBFFElectrostaticCalculationGaff&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGaff]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,101 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGaff; _Args = {const OpenBabel::OBFFElectrostaticCalculationGaff&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGaff]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,101 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,102 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:1047:45: 2025-09-09T00:39:55,102 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,102 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:55,102 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,102 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,102 ./src/forcefields/forcefieldgaff.cpp:1005:38: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:55,102 1005 | OBFFElectrostaticCalculationGaff elecalc; 2025-09-09T00:39:55,102 | ^~~~~~~ 2025-09-09T00:39:55,102 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationGaff::OBFFElectrostaticCalculationGaff(const OpenBabel::OBFFElectrostaticCalculationGaff&)’, 2025-09-09T00:39:55,103 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGaff; _Args = {const OpenBabel::OBFFElectrostaticCalculationGaff&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGaff]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:55,103 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFElectrostaticCalculationGaff; _Args = {const OpenBabel::OBFFElectrostaticCalculationGaff&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGaff]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:55,103 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGaff; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:39:55,103 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:1047:45: 2025-09-09T00:39:55,103 include/forcefields/forcefieldgaff.h:72:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:55,103 72 | class OBFFElectrostaticCalculationGaff : public OBFFCalculation2 2025-09-09T00:39:55,103 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:55,103 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:39:55,104 ./src/forcefields/forcefieldgaff.cpp:1005:38: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::rab’ was declared here 2025-09-09T00:39:55,104 1005 | OBFFElectrostaticCalculationGaff elecalc; 2025-09-09T00:39:55,104 | ^~~~~~~ 2025-09-09T00:40:01,700 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetTypes()’: 2025-09-09T00:40:01,700 ./src/forcefields/forcefieldgaff.cpp:1394:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:01,700 1394 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:40:01,700 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:01,700 1395 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:40:01,700 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:01,700 ./src/forcefields/forcefieldgaff.cpp:1403:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:01,700 1403 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:40:01,700 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:04,479 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldgaff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:40:04,479 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldgaff.o /tmp/ccdY760C.s 2025-09-09T00:40:04,485 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:05,775 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:40:05,775 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:40:05,775 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldgaff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldgaff.' 2025-09-09T00:40:05,775 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/forcefields/forcefieldghemical.cpp -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldghemical.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:40:05,779 Using built-in specs. 2025-09-09T00:40:05,780 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:05,780 Target: arm-linux-gnueabihf 2025-09-09T00:40:05,781 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:40:05,781 Thread model: posix 2025-09-09T00:40:05,781 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:05,781 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:05,782 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldghemical.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:40:05,784 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldghemical.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/forcefields/ -dumpbase forcefieldghemical.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccZAJZly.s 2025-09-09T00:40:05,797 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:05,797 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:40:05,797 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:05,798 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:05,798 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:05,798 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:05,798 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:05,798 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:05,799 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:05,799 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:05,799 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:05,799 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:05,799 #include "..." search starts here: 2025-09-09T00:40:05,799 #include <...> search starts here: 2025-09-09T00:40:05,800 /usr/include/eigen3 2025-09-09T00:40:05,800 include 2025-09-09T00:40:05,800 /usr/include/python3.13 2025-09-09T00:40:05,800 /usr/include/c++/14 2025-09-09T00:40:05,800 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:05,800 /usr/include/c++/14/backward 2025-09-09T00:40:05,800 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:05,800 /usr/local/include 2025-09-09T00:40:05,800 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:05,801 /usr/include 2025-09-09T00:40:05,801 End of search list. 2025-09-09T00:40:05,816 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:07,300 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:07,301 from include/openbabel/mol.h:43, 2025-09-09T00:40:07,301 from ./src/forcefields/forcefieldghemical.cpp:20: 2025-09-09T00:40:07,301 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:07,301 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:07,301 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:07,301 | ^ 2025-09-09T00:40:07,301 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:07,301 37 | # define UNUSED(x) x 2025-09-09T00:40:07,302 | ^ 2025-09-09T00:40:07,911 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:07,911 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:07,911 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:07,911 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:07,911 | ^ 2025-09-09T00:40:07,911 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:07,912 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:07,912 | ^~~~~~~~ 2025-09-09T00:40:07,914 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:07,915 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:07,915 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:07,915 | ^ 2025-09-09T00:40:07,915 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:07,915 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:07,915 | ^~~~~~~~ 2025-09-09T00:40:07,929 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:07,929 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:07,929 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:07,929 | ^ 2025-09-09T00:40:07,929 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:07,929 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:07,930 | ^~~~~~~~ 2025-09-09T00:40:07,934 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:07,934 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:07,934 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:07,934 | ^ 2025-09-09T00:40:07,934 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:07,934 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:07,934 | ^~~~~~~~ 2025-09-09T00:40:08,207 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:40:08,208 from include/forcefields/forcefieldghemical.h:23, 2025-09-09T00:40:08,208 from ./src/forcefields/forcefieldghemical.cpp:23: 2025-09-09T00:40:08,208 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:08,208 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:08,208 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:08,208 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:08,208 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:08,208 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:08,209 from include/openbabel/mol.h:35: 2025-09-09T00:40:08,209 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:08,209 131 | struct binary_function 2025-09-09T00:40:08,209 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:08,243 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:40:08,243 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:08,243 55 | virtual void Init(OBMol &box); 2025-09-09T00:40:08,243 | ^~~~ 2025-09-09T00:40:08,243 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:40:08,243 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:40:08,244 | ^~~~ 2025-09-09T00:40:08,254 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:08,254 229 | virtual const std::string &GetValue() const 2025-09-09T00:40:08,254 | ^~~~~~~~ 2025-09-09T00:40:08,254 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:40:08,254 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:40:08,254 76 | double GetValue (vector3 pos) const; 2025-09-09T00:40:08,254 | ^~~~~~~~ 2025-09-09T00:40:08,312 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:40:08,313 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,313 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,313 | ^ 2025-09-09T00:40:08,313 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,313 37 | # define UNUSED(x) x 2025-09-09T00:40:08,313 | ^ 2025-09-09T00:40:08,313 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:40:08,313 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,313 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,314 | ^ 2025-09-09T00:40:08,314 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,314 37 | # define UNUSED(x) x 2025-09-09T00:40:08,314 | ^ 2025-09-09T00:40:08,314 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:40:08,314 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,314 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,314 | ^ 2025-09-09T00:40:08,314 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,314 37 | # define UNUSED(x) x 2025-09-09T00:40:08,315 | ^ 2025-09-09T00:40:08,315 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:40:08,315 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,315 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,315 | ^ 2025-09-09T00:40:08,315 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,315 37 | # define UNUSED(x) x 2025-09-09T00:40:08,315 | ^ 2025-09-09T00:40:08,315 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:40:08,315 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,316 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,316 | ^ 2025-09-09T00:40:08,316 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,316 37 | # define UNUSED(x) x 2025-09-09T00:40:08,316 | ^ 2025-09-09T00:40:08,316 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:40:08,316 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,316 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,316 | ^ 2025-09-09T00:40:08,316 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,317 37 | # define UNUSED(x) x 2025-09-09T00:40:08,317 | ^ 2025-09-09T00:40:08,317 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:40:08,317 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,317 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,317 | ^ 2025-09-09T00:40:08,317 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,317 37 | # define UNUSED(x) x 2025-09-09T00:40:08,317 | ^ 2025-09-09T00:40:08,317 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:40:08,318 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:08,318 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:08,318 | ^ 2025-09-09T00:40:08,318 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:08,318 37 | # define UNUSED(x) x 2025-09-09T00:40:08,318 | ^ 2025-09-09T00:40:14,118 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Bond() [with bool = true]’: 2025-09-09T00:40:14,118 ./src/forcefields/forcefieldghemical.cpp:81:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:14,119 81 | snprintf(_logbuf, BUFF_SIZE, "%s %s %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:14,119 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,119 82 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:40:14,119 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,284 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Bond() [with bool = false]’: 2025-09-09T00:40:14,285 ./src/forcefields/forcefieldghemical.cpp:81:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:14,285 81 | snprintf(_logbuf, BUFF_SIZE, "%s %s %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:14,285 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,285 82 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:40:14,285 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,434 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Angle() [with bool = true]’: 2025-09-09T00:40:14,434 ./src/forcefields/forcefieldghemical.cpp:151:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:14,434 151 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:14,434 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,434 152 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:40:14,434 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,611 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Angle() [with bool = false]’: 2025-09-09T00:40:14,611 ./src/forcefields/forcefieldghemical.cpp:151:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:14,611 151 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:14,611 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,611 152 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:40:14,611 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,736 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Torsion() [with bool = false]’: 2025-09-09T00:40:14,736 ./src/forcefields/forcefieldghemical.cpp:231:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:14,736 231 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %s %6.3f %5.0f %8.3f %1.0f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:14,736 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,736 232 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, (*i).s, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:40:14,736 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,882 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_VDW() [with bool = false]’: 2025-09-09T00:40:14,883 ./src/forcefields/forcefieldghemical.cpp:305:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:14,883 305 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:14,883 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:14,883 306 | (*i).rab, (*i).kab, (*i).energy); 2025-09-09T00:40:14,883 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:15,175 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Electrostatic() [with bool = false]’: 2025-09-09T00:40:15,175 ./src/forcefields/forcefieldghemical.cpp:373:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:15,175 373 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:15,175 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:15,176 374 | (*i).rab, (*i).qq, (*i).energy); 2025-09-09T00:40:15,176 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:15,382 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Torsion() [with bool = true]’: 2025-09-09T00:40:15,382 ./src/forcefields/forcefieldghemical.cpp:231:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:15,382 231 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %s %6.3f %5.0f %8.3f %1.0f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:40:15,382 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:15,382 232 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, (*i).s, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:40:15,382 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,153 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,153 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:40:17,153 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,153 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,153 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,153 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2025-09-09T00:40:17,153 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,153 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,154 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,154 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,154 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:40:17,154 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:40:17,154 | ^~~~~~~~ 2025-09-09T00:40:17,154 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,154 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:40:17,154 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,154 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,155 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,155 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2025-09-09T00:40:17,155 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,155 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,155 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,155 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,155 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:40:17,155 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:40:17,155 | ^~~~~~~~ 2025-09-09T00:40:17,155 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,155 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:40:17,156 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,156 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,156 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,156 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2025-09-09T00:40:17,156 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,156 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,156 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,156 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,156 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:40:17,156 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:40:17,157 | ^~~~~~~~ 2025-09-09T00:40:17,157 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,157 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:40:17,157 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,157 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,157 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,157 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2025-09-09T00:40:17,157 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,157 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,157 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,158 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,158 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:40:17,158 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:40:17,158 | ^~~~~~~~ 2025-09-09T00:40:17,158 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,158 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,158 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:40:17,158 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,158 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,158 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,159 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2025-09-09T00:40:17,159 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,159 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,159 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,159 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,159 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:40:17,159 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:40:17,159 | ^~~~~~~~~ 2025-09-09T00:40:17,159 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,159 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,160 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:40:17,160 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,160 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,160 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,160 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2025-09-09T00:40:17,160 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,160 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,160 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,160 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,160 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:40:17,161 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:40:17,161 | ^~~~~~~~~ 2025-09-09T00:40:17,161 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:17,161 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:40:17,161 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,161 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,161 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,161 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2025-09-09T00:40:17,161 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,161 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:17,162 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,162 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,162 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:40:17,162 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:40:17,162 | ^~~~~~~~~ 2025-09-09T00:40:17,162 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,162 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,162 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:40:17,162 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,162 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,162 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,163 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2025-09-09T00:40:17,163 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,163 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,163 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,163 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,163 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:40:17,163 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:40:17,163 | ^~~~~~~~~ 2025-09-09T00:40:17,163 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,164 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,164 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:40:17,164 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,164 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,164 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,164 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2025-09-09T00:40:17,164 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,164 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,164 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,164 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,165 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:40:17,165 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:40:17,165 | ^~~~~~~~~ 2025-09-09T00:40:17,165 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:17,165 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:40:17,165 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,165 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,165 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,165 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2025-09-09T00:40:17,165 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,165 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:17,166 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,166 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,166 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:40:17,166 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:40:17,166 | ^~~~~~~~~ 2025-09-09T00:40:17,166 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,166 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,166 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:17,166 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,166 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,167 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,167 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,167 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:40:17,167 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,167 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,167 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,167 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,167 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,167 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,167 | ^~~~~~~~~~~ 2025-09-09T00:40:17,167 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,168 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,168 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:17,168 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,168 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,168 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,168 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,168 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:40:17,168 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,169 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,169 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,169 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,169 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,169 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,169 | ^~~~~~~~~~~ 2025-09-09T00:40:17,169 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:17,169 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:17,169 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,169 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,169 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,170 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,170 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:40:17,170 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,170 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:17,170 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,170 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,170 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,170 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,170 | ^~~~~~~~~~~ 2025-09-09T00:40:17,170 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:40:17,171 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,171 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,171 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,171 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,171 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:40:17,171 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,171 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:40:17,171 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,171 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,171 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,172 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,172 | ^~~~~~~~~~~ 2025-09-09T00:40:17,172 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,172 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,172 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:17,172 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,172 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,172 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,172 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,172 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:40:17,172 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,173 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,173 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,173 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,173 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,173 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,173 | ^~~~~~~~~~~ 2025-09-09T00:40:17,173 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,173 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:17,173 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:17,174 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,174 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,174 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,174 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,174 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:40:17,174 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,174 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,174 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,174 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,175 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,175 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,175 | ^~~~~~~~~~~ 2025-09-09T00:40:17,175 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:17,175 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:17,175 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,175 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,175 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,175 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,176 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:40:17,176 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,176 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:17,176 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,176 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,176 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,176 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,176 | ^~~~~~~~~~~ 2025-09-09T00:40:17,176 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:40:17,176 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:40:17,177 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,177 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,177 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,177 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:40:17,177 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,177 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:40:17,177 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,177 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,177 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:40:17,178 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:40:17,178 | ^~~~~~~~~~~ 2025-09-09T00:40:17,178 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,178 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:40:17,178 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,178 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,178 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,178 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,178 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,178 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,179 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,179 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,179 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:40:17,179 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,179 | ^~~~~~~ 2025-09-09T00:40:17,179 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,179 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:40:17,179 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,180 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,180 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,180 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,180 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,180 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,180 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,180 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,180 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:40:17,180 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,181 | ^~~~~~~ 2025-09-09T00:40:17,181 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,181 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:40:17,181 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,181 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,181 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,181 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,181 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,181 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,182 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,182 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,182 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:40:17,182 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,182 | ^~~~~~~ 2025-09-09T00:40:17,182 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2025-09-09T00:40:17,182 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,182 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,182 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,183 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,183 include/forcefields/forcefieldghemical.h:56:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::is14))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,183 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2025-09-09T00:40:17,183 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,183 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,183 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::is14))’ was declared here 2025-09-09T00:40:17,183 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,183 | ^~~~~~~ 2025-09-09T00:40:17,184 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2025-09-09T00:40:17,184 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,184 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,184 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,184 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,184 include/forcefields/forcefieldghemical.h:56:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::samering))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,184 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2025-09-09T00:40:17,184 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,184 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,184 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::samering))’ was declared here 2025-09-09T00:40:17,185 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,185 | ^~~~~~~ 2025-09-09T00:40:17,185 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2025-09-09T00:40:17,185 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,185 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,185 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,185 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,186 include/forcefields/forcefieldghemical.h:56:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,186 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2025-09-09T00:40:17,186 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,186 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,186 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::rab’ was declared here 2025-09-09T00:40:17,186 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,186 | ^~~~~~~ 2025-09-09T00:40:17,186 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,186 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:40:17,187 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,187 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,187 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:17,187 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:17,187 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,187 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,187 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,187 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,187 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,188 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:40:17,188 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,188 | ^~~~~~~ 2025-09-09T00:40:17,188 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,188 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:40:17,188 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,188 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,188 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFVDWCalculationGhemical&}; _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:17,188 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:17,189 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:40:17,189 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,189 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,189 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,189 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,189 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:40:17,189 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:40:17,189 | ^~~~~~~ 2025-09-09T00:40:17,190 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,190 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:40:17,190 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,190 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,190 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,190 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:40:17,190 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,190 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,191 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,191 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,191 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:40:17,191 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:40:17,191 | ^~~~~~~ 2025-09-09T00:40:17,191 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,191 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:40:17,191 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,191 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,192 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,192 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:40:17,192 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,192 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,192 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,192 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,192 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2025-09-09T00:40:17,192 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:40:17,192 | ^~~~~~~ 2025-09-09T00:40:17,193 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,193 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:40:17,193 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,193 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,193 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,193 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:40:17,193 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,194 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,194 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,194 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,194 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2025-09-09T00:40:17,194 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:40:17,194 | ^~~~~~~ 2025-09-09T00:40:17,194 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’, 2025-09-09T00:40:17,194 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,194 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,194 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:17,195 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:40:17,195 include/forcefields/forcefieldghemical.h:71:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,195 71 | class OBFFElectrostaticCalculationGhemical : public OBFFCalculation2 2025-09-09T00:40:17,195 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,195 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,195 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::rab’ was declared here 2025-09-09T00:40:17,195 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:40:17,195 | ^~~~~~~ 2025-09-09T00:40:17,196 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:17,196 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:40:17,196 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:17,196 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:17,196 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFElectrostaticCalculationGhemical&}; _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:17,196 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationGhemical; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:17,196 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:40:17,196 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:17,196 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:17,196 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:17,197 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:40:17,197 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2025-09-09T00:40:17,197 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:40:17,197 | ^~~~~~~ 2025-09-09T00:40:22,010 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetTypes()’: 2025-09-09T00:40:22,010 ./src/forcefields/forcefieldghemical.cpp:1001:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:22,010 1001 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:40:22,010 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:22,010 1002 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:40:22,010 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:22,010 ./src/forcefields/forcefieldghemical.cpp:1010:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:22,010 1010 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:40:22,011 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:23,883 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldghemical.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:40:23,884 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldghemical.o /tmp/ccZAJZly.s 2025-09-09T00:40:23,891 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:25,099 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:40:25,099 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:40:25,099 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldghemical.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldghemical.' 2025-09-09T00:40:25,099 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/forcefields/forcefieldmm2.cpp -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmm2.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:40:25,103 Using built-in specs. 2025-09-09T00:40:25,104 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:25,104 Target: arm-linux-gnueabihf 2025-09-09T00:40:25,104 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:40:25,105 Thread model: posix 2025-09-09T00:40:25,105 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:25,105 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:25,105 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmm2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:40:25,105 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldmm2.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/forcefields/ -dumpbase forcefieldmm2.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc4QH9qY.s 2025-09-09T00:40:25,117 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:25,117 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:40:25,117 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:25,117 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:25,118 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:25,118 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:25,119 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:25,119 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:25,119 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:25,119 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:25,119 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:25,119 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:25,120 #include "..." search starts here: 2025-09-09T00:40:25,120 #include <...> search starts here: 2025-09-09T00:40:25,120 /usr/include/eigen3 2025-09-09T00:40:25,120 include 2025-09-09T00:40:25,120 /usr/include/python3.13 2025-09-09T00:40:25,120 /usr/include/c++/14 2025-09-09T00:40:25,120 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:25,121 /usr/include/c++/14/backward 2025-09-09T00:40:25,121 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:25,121 /usr/local/include 2025-09-09T00:40:25,121 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:25,121 /usr/include 2025-09-09T00:40:25,121 End of search list. 2025-09-09T00:40:25,137 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:25,592 In file included from ./src/forcefields/forcefieldmm2.cpp:21: 2025-09-09T00:40:25,592 include/forcefields/forcefieldmm2.h:68:57: warning: multi-line comment [-Wcomment] 2025-09-09T00:40:25,593 68 | // b = atom d \ 2025-09-09T00:40:25,593 | ^ 2025-09-09T00:40:25,594 ./src/forcefields/forcefieldmm2.cpp:276:3: warning: multi-line comment [-Wcomment] 2025-09-09T00:40:25,594 276 | // \ 2025-09-09T00:40:25,594 | ^ 2025-09-09T00:40:26,646 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:26,647 from include/openbabel/mol.h:43, 2025-09-09T00:40:26,647 from ./src/forcefields/forcefieldmm2.cpp:19: 2025-09-09T00:40:26,647 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:26,647 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:26,647 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:26,647 | ^ 2025-09-09T00:40:26,647 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:26,647 37 | # define UNUSED(x) x 2025-09-09T00:40:26,647 | ^ 2025-09-09T00:40:27,262 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:27,262 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,263 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,263 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:27,263 | ^ 2025-09-09T00:40:27,263 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:27,263 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:27,263 | ^~~~~~~~ 2025-09-09T00:40:27,267 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,267 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,267 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:27,267 | ^ 2025-09-09T00:40:27,267 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:27,267 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:27,268 | ^~~~~~~~ 2025-09-09T00:40:27,282 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,282 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,282 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:27,282 | ^ 2025-09-09T00:40:27,282 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:27,282 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:27,283 | ^~~~~~~~ 2025-09-09T00:40:27,287 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,287 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,287 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:27,287 | ^ 2025-09-09T00:40:27,287 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:27,287 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:27,287 | ^~~~~~~~ 2025-09-09T00:40:27,560 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:40:27,560 from include/forcefields/forcefieldmm2.h:23: 2025-09-09T00:40:27,560 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:27,560 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:27,560 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:27,561 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:27,561 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:27,561 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:27,561 from include/openbabel/mol.h:35: 2025-09-09T00:40:27,561 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:27,561 131 | struct binary_function 2025-09-09T00:40:27,561 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:27,600 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:40:27,600 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,600 55 | virtual void Init(OBMol &box); 2025-09-09T00:40:27,600 | ^~~~ 2025-09-09T00:40:27,600 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:40:27,600 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:40:27,600 | ^~~~ 2025-09-09T00:40:27,607 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,607 229 | virtual const std::string &GetValue() const 2025-09-09T00:40:27,608 | ^~~~~~~~ 2025-09-09T00:40:27,608 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:40:27,608 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:40:27,608 76 | double GetValue (vector3 pos) const; 2025-09-09T00:40:27,608 | ^~~~~~~~ 2025-09-09T00:40:27,667 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:40:27,667 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,667 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,667 | ^ 2025-09-09T00:40:27,667 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,667 37 | # define UNUSED(x) x 2025-09-09T00:40:27,667 | ^ 2025-09-09T00:40:27,668 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:40:27,668 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,668 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,668 | ^ 2025-09-09T00:40:27,668 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,668 37 | # define UNUSED(x) x 2025-09-09T00:40:27,668 | ^ 2025-09-09T00:40:27,669 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:40:27,669 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,669 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,669 | ^ 2025-09-09T00:40:27,669 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,669 37 | # define UNUSED(x) x 2025-09-09T00:40:27,669 | ^ 2025-09-09T00:40:27,670 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:40:27,670 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,670 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,670 | ^ 2025-09-09T00:40:27,670 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,670 37 | # define UNUSED(x) x 2025-09-09T00:40:27,670 | ^ 2025-09-09T00:40:27,671 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:40:27,671 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,671 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,671 | ^ 2025-09-09T00:40:27,671 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,671 37 | # define UNUSED(x) x 2025-09-09T00:40:27,671 | ^ 2025-09-09T00:40:27,671 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:40:27,672 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,672 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,672 | ^ 2025-09-09T00:40:27,672 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,672 37 | # define UNUSED(x) x 2025-09-09T00:40:27,672 | ^ 2025-09-09T00:40:27,672 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:40:27,673 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,673 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,673 | ^ 2025-09-09T00:40:27,673 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,673 37 | # define UNUSED(x) x 2025-09-09T00:40:27,673 | ^ 2025-09-09T00:40:27,673 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:40:27,673 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:27,674 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,674 | ^ 2025-09-09T00:40:27,674 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:27,674 37 | # define UNUSED(x) x 2025-09-09T00:40:27,674 | ^ 2025-09-09T00:40:27,699 include/openbabel/forcefield.h: At global scope: 2025-09-09T00:40:27,699 include/openbabel/forcefield.h:951:20: warning: ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,699 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,699 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:27,700 include/forcefields/forcefieldmm2.h:123:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Electrostatic()’ 2025-09-09T00:40:27,700 123 | double E_Electrostatic(); 2025-09-09T00:40:27,700 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:27,700 include/openbabel/forcefield.h:944:20: warning: ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,700 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,700 | ^~~~~ 2025-09-09T00:40:27,700 include/forcefields/forcefieldmm2.h:121:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_VDW()’ 2025-09-09T00:40:27,701 121 | double E_VDW(); 2025-09-09T00:40:27,701 | ^~~~~ 2025-09-09T00:40:27,701 include/openbabel/forcefield.h:937:20: warning: ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,701 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,701 | ^~~~~ 2025-09-09T00:40:27,701 include/forcefields/forcefieldmm2.h:119:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_OOP()’ 2025-09-09T00:40:27,701 119 | double E_OOP(); 2025-09-09T00:40:27,701 | ^~~~~ 2025-09-09T00:40:27,702 include/openbabel/forcefield.h:930:20: warning: ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,702 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,702 | ^~~~~~~~~ 2025-09-09T00:40:27,702 include/forcefields/forcefieldmm2.h:117:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Torsion()’ 2025-09-09T00:40:27,702 117 | double E_Torsion(); 2025-09-09T00:40:27,702 | ^~~~~~~~~ 2025-09-09T00:40:27,702 include/openbabel/forcefield.h:923:20: warning: ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,702 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,702 | ^~~~~~~~ 2025-09-09T00:40:27,703 include/forcefields/forcefieldmm2.h:115:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_StrBnd()’ 2025-09-09T00:40:27,703 115 | double E_StrBnd(); 2025-09-09T00:40:27,703 | ^~~~~~~~ 2025-09-09T00:40:27,703 include/openbabel/forcefield.h:916:20: warning: ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,703 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,703 | ^~~~~~~ 2025-09-09T00:40:27,703 include/forcefields/forcefieldmm2.h:113:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Angle()’ 2025-09-09T00:40:27,703 113 | double E_Angle(); 2025-09-09T00:40:27,704 | ^~~~~~~ 2025-09-09T00:40:27,704 include/openbabel/forcefield.h:909:20: warning: ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,704 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,704 | ^~~~~~ 2025-09-09T00:40:27,704 include/forcefields/forcefieldmm2.h:111:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Bond()’ 2025-09-09T00:40:27,704 111 | double E_Bond(); 2025-09-09T00:40:27,704 | ^~~~~~ 2025-09-09T00:40:27,704 include/openbabel/forcefield.h:902:20: warning: ‘virtual double OpenBabel::OBForceField::Energy(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:27,705 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:27,705 | ^~~~~~ 2025-09-09T00:40:27,705 include/forcefields/forcefieldmm2.h:109:14: note: by ‘double OpenBabel::OBForceFieldMM2::Energy()’ 2025-09-09T00:40:27,705 109 | double Energy(); 2025-09-09T00:40:27,705 | ^~~~~~ 2025-09-09T00:40:27,711 include/forcefields/forcefieldmm2.h: In member function ‘virtual OpenBabel::OBForceFieldMM2* OpenBabel::OBForceFieldMM2::MakeNewInstance()’: 2025-09-09T00:40:27,711 include/forcefields/forcefieldmm2.h:97:83: warning: implicitly-declared ‘OpenBabel::OBForceFieldMM2::OBForceFieldMM2(const OpenBabel::OBForceFieldMM2&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,711 97 | virtual OBForceFieldMM2* MakeNewInstance(){ return new OBForceFieldMM2(*this); } 2025-09-09T00:40:27,711 | ^ 2025-09-09T00:40:27,711 include/forcefields/forcefieldmm2.h:107:24: note: because ‘OpenBabel::OBForceFieldMM2’ has user-provided ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’ 2025-09-09T00:40:27,711 107 | OBForceFieldMM2 &operator = (OBForceFieldMM2 &); 2025-09-09T00:40:27,711 | ^~~~~~~~ 2025-09-09T00:40:27,724 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_Angle()’: 2025-09-09T00:40:27,724 ./src/forcefields/forcefieldmm2.cpp:81:59: warning: variable ‘delta3’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:40:27,724 81 | double e, energy, force, ang, ang_ref, delta, delta2, delta3, delta4, f, dotprod, rab, rab2, rab3, rbc, rbc2, rbc3, root, dotprod_abbc; 2025-09-09T00:40:27,724 | ^~~~~~ 2025-09-09T00:40:27,737 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_OOP()’: 2025-09-09T00:40:27,737 ./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] 2025-09-09T00:40:27,738 292 | for (int idx=0; idx < _ffoutplanebendparams.size(); idx++) { 2025-09-09T00:40:27,738 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:28,850 ./src/forcefields/forcefieldmm2.cpp: In member function ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’: 2025-09-09T00:40:28,851 ./src/forcefields/forcefieldmm2.cpp:503:3: warning: control reaches end of non-void function [-Wreturn-type] 2025-09-09T00:40:28,851 503 | } 2025-09-09T00:40:28,851 | ^ 2025-09-09T00:40:36,659 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmm2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:40:36,660 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmm2.o /tmp/cc4QH9qY.s 2025-09-09T00:40:36,665 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:37,618 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:40:37,619 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:40:37,619 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmm2.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmm2.' 2025-09-09T00:40:37,623 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/forcefields/forcefieldmmff94.cpp -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmmff94.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:40:37,627 Using built-in specs. 2025-09-09T00:40:37,628 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:37,628 Target: arm-linux-gnueabihf 2025-09-09T00:40:37,629 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:40:37,629 Thread model: posix 2025-09-09T00:40:37,629 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:37,629 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:37,630 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:40:37,631 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefieldmmff94.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/forcefields/ -dumpbase forcefieldmmff94.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cchrP2yb.s 2025-09-09T00:40:37,643 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:37,644 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:40:37,644 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:37,644 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:37,645 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:37,645 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:37,645 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:37,645 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:37,646 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:37,646 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:37,646 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:37,646 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:37,646 #include "..." search starts here: 2025-09-09T00:40:37,646 #include <...> search starts here: 2025-09-09T00:40:37,647 /usr/include/eigen3 2025-09-09T00:40:37,647 include 2025-09-09T00:40:37,647 /usr/include/python3.13 2025-09-09T00:40:37,647 /usr/include/c++/14 2025-09-09T00:40:37,647 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:37,647 /usr/include/c++/14/backward 2025-09-09T00:40:37,648 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:37,648 /usr/local/include 2025-09-09T00:40:37,648 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:37,648 /usr/include 2025-09-09T00:40:37,648 End of search list. 2025-09-09T00:40:37,666 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:39,169 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:39,169 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:39,169 from ./src/forcefields/forcefieldmmff94.cpp:31: 2025-09-09T00:40:39,169 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:39,169 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:39,169 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:39,170 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:40:39,170 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:40:39,171 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:40:39,171 from /usr/include/c++/14/ios:44, 2025-09-09T00:40:39,171 from /usr/include/c++/14/ostream:40, 2025-09-09T00:40:39,171 from /usr/include/c++/14/iostream:41, 2025-09-09T00:40:39,171 from include/openbabel/obconversion.h:24: 2025-09-09T00:40:39,171 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:39,171 131 | struct binary_function 2025-09-09T00:40:39,171 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:39,348 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:39,348 from include/openbabel/mol.h:43, 2025-09-09T00:40:39,348 from ./src/forcefields/forcefieldmmff94.cpp:32: 2025-09-09T00:40:39,349 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:39,349 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:39,349 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:39,349 | ^ 2025-09-09T00:40:39,349 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:39,349 37 | # define UNUSED(x) x 2025-09-09T00:40:39,349 | ^ 2025-09-09T00:40:39,884 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:39,884 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:39,884 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:39,884 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:39,885 | ^ 2025-09-09T00:40:39,885 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:39,885 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:39,885 | ^~~~~~~~ 2025-09-09T00:40:39,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:39,889 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:39,889 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:39,890 | ^ 2025-09-09T00:40:39,890 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:39,890 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:39,890 | ^~~~~~~~ 2025-09-09T00:40:39,905 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:39,905 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:39,906 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:39,906 | ^ 2025-09-09T00:40:39,906 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:39,906 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:39,906 | ^~~~~~~~ 2025-09-09T00:40:39,913 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:39,913 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:39,913 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:39,913 | ^ 2025-09-09T00:40:39,914 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:39,914 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:39,914 | ^~~~~~~~ 2025-09-09T00:40:40,224 In file included from include/openbabel/forcefield.h:33, 2025-09-09T00:40:40,224 from include/forcefields/forcefieldmmff94.h:24, 2025-09-09T00:40:40,224 from ./src/forcefields/forcefieldmmff94.cpp:36: 2025-09-09T00:40:40,224 include/openbabel/grid.h: At global scope: 2025-09-09T00:40:40,224 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:40,224 55 | virtual void Init(OBMol &box); 2025-09-09T00:40:40,224 | ^~~~ 2025-09-09T00:40:40,225 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:40:40,225 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:40:40,225 | ^~~~ 2025-09-09T00:40:40,236 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:40,236 229 | virtual const std::string &GetValue() const 2025-09-09T00:40:40,236 | ^~~~~~~~ 2025-09-09T00:40:40,236 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:40:40,236 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:40:40,236 76 | double GetValue (vector3 pos) const; 2025-09-09T00:40:40,236 | ^~~~~~~~ 2025-09-09T00:40:40,289 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:40:40,289 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,289 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,289 | ^ 2025-09-09T00:40:40,289 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,289 37 | # define UNUSED(x) x 2025-09-09T00:40:40,289 | ^ 2025-09-09T00:40:40,290 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:40:40,290 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,290 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,290 | ^ 2025-09-09T00:40:40,290 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,290 37 | # define UNUSED(x) x 2025-09-09T00:40:40,290 | ^ 2025-09-09T00:40:40,291 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:40:40,291 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,291 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,291 | ^ 2025-09-09T00:40:40,291 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,291 37 | # define UNUSED(x) x 2025-09-09T00:40:40,291 | ^ 2025-09-09T00:40:40,292 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:40:40,292 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,292 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,292 | ^ 2025-09-09T00:40:40,292 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,292 37 | # define UNUSED(x) x 2025-09-09T00:40:40,292 | ^ 2025-09-09T00:40:40,292 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:40:40,293 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,293 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,293 | ^ 2025-09-09T00:40:40,293 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,293 37 | # define UNUSED(x) x 2025-09-09T00:40:40,293 | ^ 2025-09-09T00:40:40,293 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:40:40,293 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,294 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,294 | ^ 2025-09-09T00:40:40,294 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,294 37 | # define UNUSED(x) x 2025-09-09T00:40:40,294 | ^ 2025-09-09T00:40:40,294 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:40:40,294 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,295 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,295 | ^ 2025-09-09T00:40:40,295 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,295 37 | # define UNUSED(x) x 2025-09-09T00:40:40,295 | ^ 2025-09-09T00:40:40,295 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:40:40,295 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:40:40,295 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:40:40,295 | ^ 2025-09-09T00:40:40,296 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:40,296 37 | # define UNUSED(x) x 2025-09-09T00:40:40,296 | ^ 2025-09-09T00:40:40,555 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:40,555 ./src/forcefields/forcefieldmmff94.cpp:2790:32: warning: variable ‘bondtype1’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:40:40,555 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2025-09-09T00:40:40,555 | ^~~~~~~~~ 2025-09-09T00:40:40,555 ./src/forcefields/forcefieldmmff94.cpp:2790:43: warning: variable ‘bondtype2’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:40:40,555 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2025-09-09T00:40:40,556 | ^~~~~~~~~ 2025-09-09T00:40:40,923 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = true]’: 2025-09-09T00:40:40,923 include/forcefields/forcefieldmmff94.h:288:40: required from here 2025-09-09T00:40:40,923 288 | return gradients ? E_Bond() : E_Bond(); 2025-09-09T00:40:40,923 | ~~~~~~~~~~~~^~ 2025-09-09T00:40:40,923 ./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] 2025-09-09T00:40:40,923 140 | for (int i = 0; i < _bondcalculations.size(); ++i) { 2025-09-09T00:40:40,923 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,926 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = false]’: 2025-09-09T00:40:40,926 include/forcefields/forcefieldmmff94.h:288:58: required from here 2025-09-09T00:40:40,926 288 | return gradients ? E_Bond() : E_Bond(); 2025-09-09T00:40:40,926 | ~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,926 ./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] 2025-09-09T00:40:40,926 140 | for (int i = 0; i < _bondcalculations.size(); ++i) { 2025-09-09T00:40:40,926 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,929 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = true]’: 2025-09-09T00:40:40,929 include/forcefields/forcefieldmmff94.h:294:41: required from here 2025-09-09T00:40:40,929 294 | return gradients ? E_Angle() : E_Angle(); 2025-09-09T00:40:40,929 | ~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,929 ./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] 2025-09-09T00:40:40,929 255 | for (int i = 0; i < _anglecalculations.size(); ++i) { 2025-09-09T00:40:40,929 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,932 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = false]’: 2025-09-09T00:40:40,932 include/forcefields/forcefieldmmff94.h:294:60: required from here 2025-09-09T00:40:40,932 294 | return gradients ? E_Angle() : E_Angle(); 2025-09-09T00:40:40,932 | ~~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,932 ./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] 2025-09-09T00:40:40,932 255 | for (int i = 0; i < _anglecalculations.size(); ++i) { 2025-09-09T00:40:40,932 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,935 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = true]’: 2025-09-09T00:40:40,935 include/forcefields/forcefieldmmff94.h:300:42: required from here 2025-09-09T00:40:40,935 300 | return gradients ? E_StrBnd() : E_StrBnd(); 2025-09-09T00:40:40,935 | ~~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,935 ./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] 2025-09-09T00:40:40,935 368 | for (int i = 0; i < _strbndcalculations.size(); ++i) { 2025-09-09T00:40:40,935 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,938 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = false]’: 2025-09-09T00:40:40,938 include/forcefields/forcefieldmmff94.h:300:62: required from here 2025-09-09T00:40:40,938 300 | return gradients ? E_StrBnd() : E_StrBnd(); 2025-09-09T00:40:40,938 | ~~~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,938 ./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] 2025-09-09T00:40:40,939 368 | for (int i = 0; i < _strbndcalculations.size(); ++i) { 2025-09-09T00:40:40,939 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,941 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = true]’: 2025-09-09T00:40:40,941 include/forcefields/forcefieldmmff94.h:306:43: required from here 2025-09-09T00:40:40,941 306 | return gradients ? E_Torsion() : E_Torsion(); 2025-09-09T00:40:40,942 | ~~~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,942 ./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] 2025-09-09T00:40:40,942 504 | for (int i = 0; i < _torsioncalculations.size(); ++i) { 2025-09-09T00:40:40,942 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,945 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = false]’: 2025-09-09T00:40:40,945 include/forcefields/forcefieldmmff94.h:306:64: required from here 2025-09-09T00:40:40,945 306 | return gradients ? E_Torsion() : E_Torsion(); 2025-09-09T00:40:40,945 | ~~~~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,945 ./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] 2025-09-09T00:40:40,945 504 | for (int i = 0; i < _torsioncalculations.size(); ++i) { 2025-09-09T00:40:40,945 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,948 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = true]’: 2025-09-09T00:40:40,948 include/forcefields/forcefieldmmff94.h:312:39: required from here 2025-09-09T00:40:40,948 312 | return gradients ? E_OOP() : E_OOP(); 2025-09-09T00:40:40,948 | ~~~~~~~~~~~^~ 2025-09-09T00:40:40,948 ./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] 2025-09-09T00:40:40,948 602 | for (int i = 0; i < _oopcalculations.size(); ++i) { 2025-09-09T00:40:40,949 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,951 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = false]’: 2025-09-09T00:40:40,951 include/forcefields/forcefieldmmff94.h:312:56: required from here 2025-09-09T00:40:40,952 312 | return gradients ? E_OOP() : E_OOP(); 2025-09-09T00:40:40,952 | ~~~~~~~~~~~~^~ 2025-09-09T00:40:40,952 ./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] 2025-09-09T00:40:40,952 602 | for (int i = 0; i < _oopcalculations.size(); ++i) { 2025-09-09T00:40:40,952 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,954 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = true]’: 2025-09-09T00:40:40,955 include/forcefields/forcefieldmmff94.h:318:39: required from here 2025-09-09T00:40:40,955 318 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:40:40,955 | ~~~~~~~~~~~^~ 2025-09-09T00:40:40,955 ./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] 2025-09-09T00:40:40,955 699 | for (int i = 0; i < _vdwcalculations.size(); ++i) { 2025-09-09T00:40:40,955 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,957 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = false]’: 2025-09-09T00:40:40,958 include/forcefields/forcefieldmmff94.h:318:56: required from here 2025-09-09T00:40:40,958 318 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:40:40,958 | ~~~~~~~~~~~~^~ 2025-09-09T00:40:40,958 ./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] 2025-09-09T00:40:40,958 699 | for (int i = 0; i < _vdwcalculations.size(); ++i) { 2025-09-09T00:40:40,958 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,960 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = true]’: 2025-09-09T00:40:40,961 include/forcefields/forcefieldmmff94.h:324:49: required from here 2025-09-09T00:40:40,961 324 | return gradients ? E_Electrostatic() : E_Electrostatic(); 2025-09-09T00:40:40,961 | ~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,961 ./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] 2025-09-09T00:40:40,961 785 | for (int i = 0; i < _electrostaticcalculations.size(); ++i) { 2025-09-09T00:40:40,961 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:40,963 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = false]’: 2025-09-09T00:40:40,963 include/forcefields/forcefieldmmff94.h:324:76: required from here 2025-09-09T00:40:40,964 324 | return gradients ? E_Electrostatic() : E_Electrostatic(); 2025-09-09T00:40:40,964 | ~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:40:40,964 ./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] 2025-09-09T00:40:40,964 785 | for (int i = 0; i < _electrostaticcalculations.size(); ++i) { 2025-09-09T00:40:40,964 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:42,221 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘int OpenBabel::OBForceFieldMMFF94::GetStrBndType(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*)’: 2025-09-09T00:40:42,221 ./src/forcefields/forcefieldmmff94.cpp:4540:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:40:42,221 4540 | if (btbc) { 2025-09-09T00:40:42,221 | ^~ 2025-09-09T00:40:42,222 ./src/forcefields/forcefieldmmff94.cpp:4548:5: note: here 2025-09-09T00:40:42,222 4548 | case 2: 2025-09-09T00:40:42,222 | ^~~~ 2025-09-09T00:40:42,222 ./src/forcefields/forcefieldmmff94.cpp:4565:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:40:42,222 4565 | if (btbc) { 2025-09-09T00:40:42,222 | ^~ 2025-09-09T00:40:42,222 ./src/forcefields/forcefieldmmff94.cpp:4573:5: note: here 2025-09-09T00:40:42,222 4573 | case 6: 2025-09-09T00:40:42,223 | ^~~~ 2025-09-09T00:40:42,223 ./src/forcefields/forcefieldmmff94.cpp:4584:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:40:42,223 4584 | if (btbc) { 2025-09-09T00:40:42,223 | ^~ 2025-09-09T00:40:42,223 ./src/forcefields/forcefieldmmff94.cpp:4592:5: note: here 2025-09-09T00:40:42,223 4592 | case 8: 2025-09-09T00:40:42,223 | ^~~~ 2025-09-09T00:40:46,638 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘bool OpenBabel::OBForceFieldMMFF94::PerceiveAromatic()’: 2025-09-09T00:40:46,638 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:46,638 1443 | ringbond = _mol.GetBond(first_rj, index); 2025-09-09T00:40:46,638 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:40:46,639 ./src/forcefields/forcefieldmmff94.cpp:1380:12: note: ‘index’ was declared here 2025-09-09T00:40:46,639 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2025-09-09T00:40:46,639 | ^~~~~ 2025-09-09T00:40:46,639 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘first_rj’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:46,639 1443 | ringbond = _mol.GetBond(first_rj, index); 2025-09-09T00:40:46,639 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:40:46,640 ./src/forcefields/forcefieldmmff94.cpp:1380:29: note: ‘first_rj’ was declared here 2025-09-09T00:40:46,640 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2025-09-09T00:40:46,640 | ^~~~~~~~ 2025-09-09T00:40:47,685 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = true]’: 2025-09-09T00:40:47,685 ./src/forcefields/forcefieldmmff94.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:47,685 152 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:47,685 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,685 153 | atoi(_bondcalculations[i].a->GetType()), atoi(_bondcalculations[i].b->GetType()), 2025-09-09T00:40:47,685 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,685 154 | _bondcalculations[i].bt, _bondcalculations[i].rab, _bondcalculations[i].r0, 2025-09-09T00:40:47,685 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,685 155 | _bondcalculations[i].kb, _bondcalculations[i].delta, 2025-09-09T00:40:47,686 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,686 156 | 143.9325 * 0.5 * _bondcalculations[i].energy); 2025-09-09T00:40:47,686 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,866 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = false]’: 2025-09-09T00:40:47,866 ./src/forcefields/forcefieldmmff94.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:47,866 152 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:47,866 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,866 153 | atoi(_bondcalculations[i].a->GetType()), atoi(_bondcalculations[i].b->GetType()), 2025-09-09T00:40:47,866 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,867 154 | _bondcalculations[i].bt, _bondcalculations[i].rab, _bondcalculations[i].r0, 2025-09-09T00:40:47,867 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,867 155 | _bondcalculations[i].kb, _bondcalculations[i].delta, 2025-09-09T00:40:47,867 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:47,867 156 | 143.9325 * 0.5 * _bondcalculations[i].energy); 2025-09-09T00:40:47,867 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,042 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = true]’: 2025-09-09T00:40:48,042 ./src/forcefields/forcefieldmmff94.cpp:269:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:48,042 269 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:48,042 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,042 270 | atoi(_anglecalculations[i].a->GetType()), atoi(_anglecalculations[i].b->GetType()), 2025-09-09T00:40:48,042 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,042 271 | atoi(_anglecalculations[i].c->GetType()), _anglecalculations[i].at, 2025-09-09T00:40:48,042 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,042 272 | _anglecalculations[i].theta, _anglecalculations[i].theta0, 2025-09-09T00:40:48,042 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,043 273 | _anglecalculations[i].ka, _anglecalculations[i].delta, 2025-09-09T00:40:48,043 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,043 274 | _anglecalculations[i].energy); 2025-09-09T00:40:48,043 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,270 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = false]’: 2025-09-09T00:40:48,270 ./src/forcefields/forcefieldmmff94.cpp:269:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:48,270 269 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:48,270 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,270 270 | atoi(_anglecalculations[i].a->GetType()), atoi(_anglecalculations[i].b->GetType()), 2025-09-09T00:40:48,270 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,270 271 | atoi(_anglecalculations[i].c->GetType()), _anglecalculations[i].at, 2025-09-09T00:40:48,270 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,270 272 | _anglecalculations[i].theta, _anglecalculations[i].theta0, 2025-09-09T00:40:48,270 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,271 273 | _anglecalculations[i].ka, _anglecalculations[i].delta, 2025-09-09T00:40:48,271 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,271 274 | _anglecalculations[i].energy); 2025-09-09T00:40:48,271 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,469 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = true]’: 2025-09-09T00:40:48,469 ./src/forcefields/forcefieldmmff94.cpp:382:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:48,469 382 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:48,469 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,469 383 | atoi(_strbndcalculations[i].a->GetType()), atoi(_strbndcalculations[i].b->GetType()), 2025-09-09T00:40:48,470 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,470 384 | atoi(_strbndcalculations[i].c->GetType()), _strbndcalculations[i].sbt, 2025-09-09T00:40:48,470 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,470 385 | _strbndcalculations[i].theta, _strbndcalculations[i].delta_theta, 2025-09-09T00:40:48,470 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,470 386 | _strbndcalculations[i].kbaABC, _strbndcalculations[i].kbaCBA, 2025-09-09T00:40:48,470 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,470 387 | 2.51210 * _strbndcalculations[i].energy); 2025-09-09T00:40:48,470 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,735 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = false]’: 2025-09-09T00:40:48,735 ./src/forcefields/forcefieldmmff94.cpp:382:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:48,735 382 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:48,735 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,735 383 | atoi(_strbndcalculations[i].a->GetType()), atoi(_strbndcalculations[i].b->GetType()), 2025-09-09T00:40:48,735 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,736 384 | atoi(_strbndcalculations[i].c->GetType()), _strbndcalculations[i].sbt, 2025-09-09T00:40:48,736 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,736 385 | _strbndcalculations[i].theta, _strbndcalculations[i].delta_theta, 2025-09-09T00:40:48,736 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,736 386 | _strbndcalculations[i].kbaABC, _strbndcalculations[i].kbaCBA, 2025-09-09T00:40:48,736 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,736 387 | 2.51210 * _strbndcalculations[i].energy); 2025-09-09T00:40:48,736 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,953 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = true]’: 2025-09-09T00:40:48,953 ./src/forcefields/forcefieldmmff94.cpp:519:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:48,953 519 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %d %8.3f %6.3f %6.3f %6.3f %8.3f\n", 2025-09-09T00:40:48,953 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,953 520 | atoi(_torsioncalculations[i].a->GetType()), atoi(_torsioncalculations[i].b->GetType()), 2025-09-09T00:40:48,953 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,954 521 | atoi(_torsioncalculations[i].c->GetType()), atoi(_torsioncalculations[i].d->GetType()), 2025-09-09T00:40:48,954 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,954 522 | _torsioncalculations[i].tt, _torsioncalculations[i].tor, _torsioncalculations[i].v1, 2025-09-09T00:40:48,954 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:48,954 523 | _torsioncalculations[i].v2, _torsioncalculations[i].v3, 0.5 * _torsioncalculations[i].energy); 2025-09-09T00:40:48,954 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,220 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = false]’: 2025-09-09T00:40:49,221 ./src/forcefields/forcefieldmmff94.cpp:519:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:49,221 519 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %d %8.3f %6.3f %6.3f %6.3f %8.3f\n", 2025-09-09T00:40:49,221 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,221 520 | atoi(_torsioncalculations[i].a->GetType()), atoi(_torsioncalculations[i].b->GetType()), 2025-09-09T00:40:49,221 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,221 521 | atoi(_torsioncalculations[i].c->GetType()), atoi(_torsioncalculations[i].d->GetType()), 2025-09-09T00:40:49,221 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,221 522 | _torsioncalculations[i].tt, _torsioncalculations[i].tor, _torsioncalculations[i].v1, 2025-09-09T00:40:49,221 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,221 523 | _torsioncalculations[i].v2, _torsioncalculations[i].v3, 0.5 * _torsioncalculations[i].energy); 2025-09-09T00:40:49,221 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,399 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = false]’: 2025-09-09T00:40:49,400 ./src/forcefields/forcefieldmmff94.cpp:617:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:49,400 617 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d 0 %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:49,400 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,400 618 | atoi(_oopcalculations[i].a->GetType()), atoi(_oopcalculations[i].b->GetType()), 2025-09-09T00:40:49,400 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,400 619 | atoi(_oopcalculations[i].c->GetType()), atoi(_oopcalculations[i].d->GetType()), 2025-09-09T00:40:49,400 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,400 620 | _oopcalculations[i].angle, _oopcalculations[i].koop, 2025-09-09T00:40:49,400 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,400 621 | 0.043844 * 0.5 * _oopcalculations[i].energy); 2025-09-09T00:40:49,401 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,731 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = false]’: 2025-09-09T00:40:49,731 ./src/forcefields/forcefieldmmff94.cpp:716:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:49,731 716 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:49,731 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,731 717 | atoi(_vdwcalculations[i].a->GetType()), atoi(_vdwcalculations[i].b->GetType()), 2025-09-09T00:40:49,731 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:49,731 718 | _vdwcalculations[i].rab, _vdwcalculations[i].R_AB, _vdwcalculations[i].epsilon, _vdwcalculations[i].energy); 2025-09-09T00:40:49,732 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,066 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = false]’: 2025-09-09T00:40:50,066 ./src/forcefields/forcefieldmmff94.cpp:802:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:50,066 802 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:50,066 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,066 803 | atoi(_electrostaticcalculations[i].a->GetType()), atoi(_electrostaticcalculations[i].b->GetType()), 2025-09-09T00:40:50,067 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,067 804 | _electrostaticcalculations[i].rab, _electrostaticcalculations[i].a->GetPartialCharge(), 2025-09-09T00:40:50,067 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,067 805 | _electrostaticcalculations[i].b->GetPartialCharge(), _electrostaticcalculations[i].energy); 2025-09-09T00:40:50,067 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,289 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = true]’: 2025-09-09T00:40:50,289 ./src/forcefields/forcefieldmmff94.cpp:617:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:40:50,290 617 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d 0 %8.3f %8.3f %8.3f\n", 2025-09-09T00:40:50,290 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,290 618 | atoi(_oopcalculations[i].a->GetType()), atoi(_oopcalculations[i].b->GetType()), 2025-09-09T00:40:50,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,290 619 | atoi(_oopcalculations[i].c->GetType()), atoi(_oopcalculations[i].d->GetType()), 2025-09-09T00:40:50,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,290 620 | _oopcalculations[i].angle, _oopcalculations[i].koop, 2025-09-09T00:40:50,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:50,290 621 | 0.043844 * 0.5 * _oopcalculations[i].energy); 2025-09-09T00:40:50,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,128 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,128 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:40:52,128 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,128 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,128 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,128 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2025-09-09T00:40:52,128 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,128 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,129 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,129 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,129 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:40:52,129 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:40:52,129 | ^~~~~~~~ 2025-09-09T00:40:52,130 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,130 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:40:52,130 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,130 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,130 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,130 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2025-09-09T00:40:52,130 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,131 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,131 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,131 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,131 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:40:52,131 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:40:52,131 | ^~~~~~~~ 2025-09-09T00:40:52,132 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,132 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:40:52,132 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,132 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,132 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,132 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2025-09-09T00:40:52,132 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,132 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,132 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,133 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,133 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:40:52,133 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:40:52,133 | ^~~~~~~~ 2025-09-09T00:40:52,133 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,134 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:40:52,134 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,134 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,134 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,134 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2025-09-09T00:40:52,134 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,134 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,134 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,134 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,135 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:40:52,135 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:40:52,135 | ^~~~~~~~ 2025-09-09T00:40:52,136 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,136 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,136 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:40:52,137 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,137 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,137 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,137 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,137 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,137 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,137 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,137 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,138 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:40:52,138 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,138 | ^~~~~~~~~ 2025-09-09T00:40:52,138 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,139 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,139 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:40:52,139 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,139 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,139 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,139 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,139 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,139 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,139 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,150 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,150 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:40:52,150 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,150 | ^~~~~~~~~ 2025-09-09T00:40:52,150 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,150 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,150 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:40:52,150 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,150 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,151 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,151 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,151 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,151 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,151 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,151 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,151 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:40:52,151 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,151 | ^~~~~~~~~ 2025-09-09T00:40:52,151 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:52,151 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:40:52,152 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,152 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,152 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,152 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,152 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,152 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:52,152 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,152 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,152 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:40:52,152 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,152 | ^~~~~~~~~ 2025-09-09T00:40:52,153 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2025-09-09T00:40:52,153 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,153 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,153 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,153 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,153 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,153 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,153 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,153 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::theta’ was declared here 2025-09-09T00:40:52,153 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,154 | ^~~~~~~~~ 2025-09-09T00:40:52,154 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2025-09-09T00:40:52,154 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,154 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,154 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,154 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,154 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,154 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,154 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,154 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,154 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::delta’ was declared here 2025-09-09T00:40:52,154 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,155 | ^~~~~~~~~ 2025-09-09T00:40:52,155 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,155 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,155 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:40:52,155 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,155 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,155 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,155 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,155 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,155 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,156 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,156 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,156 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,156 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:40:52,156 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,156 | ^~~~~~~~~ 2025-09-09T00:40:52,156 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,156 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,156 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:40:52,156 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,156 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,157 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,157 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,157 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,157 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,157 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,157 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,157 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,157 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:40:52,157 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,157 | ^~~~~~~~~ 2025-09-09T00:40:52,157 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:52,157 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:40:52,158 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,158 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,158 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,158 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,158 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:40:52,158 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,158 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:52,158 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,158 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,158 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:40:52,158 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:40:52,159 | ^~~~~~~~~ 2025-09-09T00:40:52,159 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,159 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,159 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:40:52,159 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,159 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,159 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,159 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,159 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,159 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,160 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,160 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,160 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:40:52,160 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,160 | ^~~~~~~~~~ 2025-09-09T00:40:52,160 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,160 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,160 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:40:52,160 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,160 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,161 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,161 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,161 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,161 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,161 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,161 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,161 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,161 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,162 | ^~~~~~~~~~ 2025-09-09T00:40:52,162 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,162 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,162 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:40:52,162 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,162 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,162 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,162 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,162 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,163 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,163 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,163 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,163 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,163 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,163 | ^~~~~~~~~~ 2025-09-09T00:40:52,163 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:52,163 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:40:52,164 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,164 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,164 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,164 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,164 include/openbabel/forcefield.h:170:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,164 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:52,164 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,164 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,165 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,165 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,165 | ^~~~~~~~~~ 2025-09-09T00:40:52,165 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,165 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,165 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,165 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,165 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,166 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,166 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,166 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,166 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,166 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_theta’ was declared here 2025-09-09T00:40:52,166 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,166 | ^~~~~~~~~~ 2025-09-09T00:40:52,166 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,167 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,167 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,167 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,167 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,167 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,167 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,167 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,167 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,167 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rab’ was declared here 2025-09-09T00:40:52,168 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,168 | ^~~~~~~~~~ 2025-09-09T00:40:52,168 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,168 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,168 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,168 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,168 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,168 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,169 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,169 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,169 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,169 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rbc’ was declared here 2025-09-09T00:40:52,169 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,169 | ^~~~~~~~~~ 2025-09-09T00:40:52,169 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,169 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,169 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,170 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,170 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,170 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,170 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,170 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,170 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,170 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::theta’ was declared here 2025-09-09T00:40:52,170 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,171 | ^~~~~~~~~~ 2025-09-09T00:40:52,171 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,171 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,171 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,171 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,171 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,171 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,171 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,171 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,172 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,172 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rab’ was declared here 2025-09-09T00:40:52,172 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,172 | ^~~~~~~~~~ 2025-09-09T00:40:52,172 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,172 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,172 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,173 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,173 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,173 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,173 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,173 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,173 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,173 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rbc’ was declared here 2025-09-09T00:40:52,173 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,173 | ^~~~~~~~~~ 2025-09-09T00:40:52,174 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,174 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,174 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,174 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,174 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,174 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,174 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,175 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,175 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,175 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,175 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,175 | ^~~~~~~~~~ 2025-09-09T00:40:52,175 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,175 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,175 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,176 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,176 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,176 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,176 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,176 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,176 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,176 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,176 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,177 | ^~~~~~~~~~ 2025-09-09T00:40:52,177 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,177 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,177 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,177 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,177 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,177 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,177 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,178 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,178 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,178 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,178 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,178 | ^~~~~~~~~~ 2025-09-09T00:40:52,178 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,178 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,179 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,179 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,179 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,179 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,179 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,180 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,180 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,180 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,180 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,180 | ^~~~~~~~~~ 2025-09-09T00:40:52,180 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,180 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,180 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,181 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,181 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,181 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,181 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,181 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,181 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,181 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,181 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,182 | ^~~~~~~~~~ 2025-09-09T00:40:52,182 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,182 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,182 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,182 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,182 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,182 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,182 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,182 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,182 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,183 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,183 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,183 | ^~~~~~~~~~ 2025-09-09T00:40:52,183 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,183 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,183 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,183 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,183 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,183 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,184 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,184 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,184 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,184 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,184 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,184 | ^~~~~~~~~~ 2025-09-09T00:40:52,184 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,184 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,184 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:40:52,185 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,185 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,185 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,185 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,185 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,185 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,185 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,185 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,185 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,186 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,186 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,186 | ^~~~~~~~~~ 2025-09-09T00:40:52,186 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,186 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,186 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:40:52,186 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,186 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,187 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,187 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,187 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,187 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,187 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,187 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,187 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,187 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,187 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,187 | ^~~~~~~~~~ 2025-09-09T00:40:52,188 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:52,188 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:40:52,188 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,188 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,188 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,188 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,188 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,188 include/openbabel/forcefield.h:170:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,189 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:52,189 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,189 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,189 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,189 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,189 | ^~~~~~~~~~ 2025-09-09T00:40:52,189 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,189 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,190 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,190 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,190 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,190 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,190 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,190 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,190 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,190 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,190 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,190 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,191 | ^~~~~~~~~~ 2025-09-09T00:40:52,191 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,191 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,191 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,191 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,191 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,191 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,191 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,192 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,192 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,192 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,192 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,192 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,192 | ^~~~~~~~~~ 2025-09-09T00:40:52,192 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,192 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,192 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,193 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,193 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,193 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,193 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,193 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,193 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,193 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,193 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,193 | ^~~~~~~~~~ 2025-09-09T00:40:52,194 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,194 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,194 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,194 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,194 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,194 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,194 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,194 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,194 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,195 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,195 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,195 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,195 | ^~~~~~~~~~ 2025-09-09T00:40:52,195 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,195 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,195 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,195 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,195 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,195 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,196 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,196 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,196 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,196 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,196 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,196 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,196 | ^~~~~~~~~~ 2025-09-09T00:40:52,196 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,196 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,197 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,197 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,197 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,197 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,197 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,197 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,197 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,198 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,198 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,198 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,198 | ^~~~~~~~~~ 2025-09-09T00:40:52,198 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:40:52,198 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,198 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,198 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:40:52,199 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFStrBndCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:40:52,199 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:40:52,199 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,199 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:40:52,199 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,199 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,199 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:40:52,199 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:40:52,199 | ^~~~~~~~~~ 2025-09-09T00:40:52,200 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,200 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,200 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:52,200 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2025-09-09T00:40:52,200 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,200 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,200 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,200 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2025-09-09T00:40:52,200 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,201 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,201 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,201 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,201 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2025-09-09T00:40:52,201 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2025-09-09T00:40:52,201 | ^~~~~~~~~~~ 2025-09-09T00:40:52,201 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,201 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:40:52,201 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:52,202 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2025-09-09T00:40:52,202 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,202 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,202 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,202 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2025-09-09T00:40:52,202 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,202 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,202 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,202 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,203 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2025-09-09T00:40:52,203 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2025-09-09T00:40:52,203 | ^~~~~~~~~~~ 2025-09-09T00:40:52,203 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:40:52,203 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:40:52,203 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2025-09-09T00:40:52,203 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,203 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,204 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFTorsionCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,204 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2025-09-09T00:40:52,204 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,204 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:40:52,204 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,204 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,204 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2025-09-09T00:40:52,204 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2025-09-09T00:40:52,204 | ^~~~~~~~~~~ 2025-09-09T00:40:52,205 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:40:52,205 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationMMFF94::OBFFVDWCalculationMMFF94(const OpenBabel::OBFFVDWCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:78:9, 2025-09-09T00:40:52,205 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationMMFF94; _Args = {const OpenBabel::OBFFVDWCalculationMMFF94&}; _Tp = OpenBabel::OBFFVDWCalculationMMFF94]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,205 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationMMFF94; _Args = {const OpenBabel::OBFFVDWCalculationMMFF94&}; _Tp = OpenBabel::OBFFVDWCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,205 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,205 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3599:33: 2025-09-09T00:40:52,205 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,205 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:40:52,206 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,206 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,206 ./src/forcefields/forcefieldmmff94.cpp:3475:30: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:40:52,206 3475 | OBFFVDWCalculationMMFF94 vdwcalc; 2025-09-09T00:40:52,206 | ^~~~~~~ 2025-09-09T00:40:52,206 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationMMFF94::OBFFVDWCalculationMMFF94(const OpenBabel::OBFFVDWCalculationMMFF94&)’, 2025-09-09T00:40:52,206 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationMMFF94; _Args = {const OpenBabel::OBFFVDWCalculationMMFF94&}; _Tp = OpenBabel::OBFFVDWCalculationMMFF94]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:40:52,206 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFVDWCalculationMMFF94; _Args = {const OpenBabel::OBFFVDWCalculationMMFF94&}; _Tp = OpenBabel::OBFFVDWCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:40:52,206 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFVDWCalculationMMFF94; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:40:52,206 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3599:33: 2025-09-09T00:40:52,207 include/forcefields/forcefieldmmff94.h:78:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:52,207 78 | class OBFFVDWCalculationMMFF94 : public OBFFCalculation2 2025-09-09T00:40:52,207 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:40:52,207 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:40:52,207 ./src/forcefields/forcefieldmmff94.cpp:3475:30: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::rab’ was declared here 2025-09-09T00:40:52,207 3475 | OBFFVDWCalculationMMFF94 vdwcalc; 2025-09-09T00:40:52,207 | ^~~~~~~ 2025-09-09T00:41:06,100 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’: 2025-09-09T00:41:06,100 ./src/forcefields/forcefieldmmff94.cpp:4194:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:06,100 4194 | snprintf(_logbuf, BUFF_SIZE, "%2d %3d %4d %3d %3d XXX FAILED XXX", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetHyb(), 2025-09-09T00:41:06,100 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,100 4195 | _mol.GetAtom(ni)->IsAromatic(), atoi(_mol.GetAtom(ni)->GetType()), *i); 2025-09-09T00:41:06,100 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,100 ./src/forcefields/forcefieldmmff94.cpp:4191:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:06,100 4191 | snprintf(_logbuf, BUFF_SIZE, "%2d %3d %4d %3d %3d PASSED", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetHyb(), 2025-09-09T00:41:06,100 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,101 4192 | _mol.GetAtom(ni)->IsAromatic(), atoi(_mol.GetAtom(ni)->GetType()), *i); 2025-09-09T00:41:06,101 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,101 ./src/forcefields/forcefieldmmff94.cpp:4227:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:06,101 4227 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f XXX FAILED XXX", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:41:06,101 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,101 ./src/forcefields/forcefieldmmff94.cpp:4225:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:06,101 4225 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f PASSED", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:41:06,101 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,101 ./src/forcefields/forcefieldmmff94.cpp:4259:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:06,101 4259 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f XXX FAILED XXX", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:41:06,101 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,101 ./src/forcefields/forcefieldmmff94.cpp:4257:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:06,102 4257 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f PASSED", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:41:06,102 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,243 ./src/forcefields/forcefieldmmff94.cpp:4316:13: warning: ‘etot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,244 4316 | delta = (Energy() - etot); 2025-09-09T00:41:06,244 | ~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,244 ./src/forcefields/forcefieldmmff94.cpp:3989:12: note: ‘etot’ was declared here 2025-09-09T00:41:06,244 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,244 | ^~~~ 2025-09-09T00:41:06,245 ./src/forcefields/forcefieldmmff94.cpp:4287:13: warning: ‘ebond’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,245 4287 | delta = (E_Bond() - ebond); 2025-09-09T00:41:06,245 | ~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,245 ./src/forcefields/forcefieldmmff94.cpp:3989:18: note: ‘ebond’ was declared here 2025-09-09T00:41:06,245 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,245 | ^~~~~ 2025-09-09T00:41:06,246 ./src/forcefields/forcefieldmmff94.cpp:4291:13: warning: ‘eangle’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,246 4291 | delta = (E_Angle() - eangle); 2025-09-09T00:41:06,246 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,246 ./src/forcefields/forcefieldmmff94.cpp:3989:25: note: ‘eangle’ was declared here 2025-09-09T00:41:06,246 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,246 | ^~~~~~ 2025-09-09T00:41:06,247 ./src/forcefields/forcefieldmmff94.cpp:4299:13: warning: ‘eoop’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,247 4299 | delta = (E_OOP() - eoop); 2025-09-09T00:41:06,247 | ~~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,247 ./src/forcefields/forcefieldmmff94.cpp:3989:33: note: ‘eoop’ was declared here 2025-09-09T00:41:06,247 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,247 | ^~~~ 2025-09-09T00:41:06,248 ./src/forcefields/forcefieldmmff94.cpp:4295:13: warning: ‘estbn’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,248 4295 | delta = (E_StrBnd() - estbn); 2025-09-09T00:41:06,248 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,248 ./src/forcefields/forcefieldmmff94.cpp:3989:39: note: ‘estbn’ was declared here 2025-09-09T00:41:06,248 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,248 | ^~~~~ 2025-09-09T00:41:06,248 ./src/forcefields/forcefieldmmff94.cpp:4303:13: warning: ‘etor’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,249 4303 | delta = (E_Torsion() - etor); 2025-09-09T00:41:06,249 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,249 ./src/forcefields/forcefieldmmff94.cpp:3989:46: note: ‘etor’ was declared here 2025-09-09T00:41:06,249 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,249 | ^~~~ 2025-09-09T00:41:06,249 ./src/forcefields/forcefieldmmff94.cpp:4307:13: warning: ‘evdw’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,250 4307 | delta = (E_VDW() - evdw); 2025-09-09T00:41:06,250 | ~~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,250 ./src/forcefields/forcefieldmmff94.cpp:3989:52: note: ‘evdw’ was declared here 2025-09-09T00:41:06,250 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,250 | ^~~~ 2025-09-09T00:41:06,250 ./src/forcefields/forcefieldmmff94.cpp:4311:13: warning: ‘eeq’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:06,251 4311 | delta = (E_Electrostatic() - eeq); 2025-09-09T00:41:06,251 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:06,251 ./src/forcefields/forcefieldmmff94.cpp:3989:58: note: ‘eeq’ was declared here 2025-09-09T00:41:06,251 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:41:06,251 | ^~~ 2025-09-09T00:41:08,249 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:41:08,250 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmmff94.o /tmp/cchrP2yb.s 2025-09-09T00:41:08,255 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:10,412 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:41:10,412 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:41:10,413 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmmff94.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefieldmmff94.' 2025-09-09T00:41:10,419 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/forcefields/forcefielduff.cpp -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefielduff.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:41:10,423 Using built-in specs. 2025-09-09T00:41:10,424 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:10,424 Target: arm-linux-gnueabihf 2025-09-09T00:41:10,425 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:41:10,425 Thread model: posix 2025-09-09T00:41:10,425 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:10,425 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:10,426 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefielduff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:41:10,427 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/forcefields/forcefielduff.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/forcefields/ -dumpbase forcefielduff.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc81jEZH.s 2025-09-09T00:41:10,439 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:10,439 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:41:10,440 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:10,440 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:10,441 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:10,442 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:10,442 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:10,442 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:10,442 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:10,443 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:10,443 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:10,443 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:10,444 #include "..." search starts here: 2025-09-09T00:41:10,444 #include <...> search starts here: 2025-09-09T00:41:10,444 /usr/include/eigen3 2025-09-09T00:41:10,444 include 2025-09-09T00:41:10,445 /usr/include/python3.13 2025-09-09T00:41:10,445 /usr/include/c++/14 2025-09-09T00:41:10,445 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:10,445 /usr/include/c++/14/backward 2025-09-09T00:41:10,445 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:10,446 /usr/local/include 2025-09-09T00:41:10,446 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:10,446 /usr/include 2025-09-09T00:41:10,446 End of search list. 2025-09-09T00:41:10,465 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:11,963 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:11,963 from include/openbabel/mol.h:43, 2025-09-09T00:41:11,963 from ./src/forcefields/forcefielduff.cpp:21: 2025-09-09T00:41:11,964 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:11,964 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:11,964 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:11,964 | ^ 2025-09-09T00:41:11,964 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:11,964 37 | # define UNUSED(x) x 2025-09-09T00:41:11,964 | ^ 2025-09-09T00:41:12,575 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:12,575 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:12,575 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:12,576 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:12,576 | ^ 2025-09-09T00:41:12,576 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:12,576 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:12,576 | ^~~~~~~~ 2025-09-09T00:41:12,580 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:12,580 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:12,580 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:12,581 | ^ 2025-09-09T00:41:12,581 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:12,581 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:12,581 | ^~~~~~~~ 2025-09-09T00:41:12,595 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:12,596 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:12,596 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:12,596 | ^ 2025-09-09T00:41:12,596 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:12,596 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:12,596 | ^~~~~~~~ 2025-09-09T00:41:12,601 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:12,601 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:12,602 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:12,602 | ^ 2025-09-09T00:41:12,602 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:12,602 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:12,602 | ^~~~~~~~ 2025-09-09T00:41:12,876 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:41:12,876 from include/forcefields/forcefielduff.h:24, 2025-09-09T00:41:12,876 from ./src/forcefields/forcefielduff.cpp:24: 2025-09-09T00:41:12,876 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:12,877 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:12,877 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:12,877 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:12,877 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:12,878 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:12,878 from include/openbabel/mol.h:35: 2025-09-09T00:41:12,878 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:12,878 131 | struct binary_function 2025-09-09T00:41:12,878 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:12,913 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:41:12,913 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:41:12,913 55 | virtual void Init(OBMol &box); 2025-09-09T00:41:12,913 | ^~~~ 2025-09-09T00:41:12,913 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:41:12,914 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:41:12,914 | ^~~~ 2025-09-09T00:41:12,925 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:41:12,925 229 | virtual const std::string &GetValue() const 2025-09-09T00:41:12,925 | ^~~~~~~~ 2025-09-09T00:41:12,925 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:41:12,925 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:41:12,925 76 | double GetValue (vector3 pos) const; 2025-09-09T00:41:12,926 | ^~~~~~~~ 2025-09-09T00:41:12,984 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:41:12,984 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,985 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,985 | ^ 2025-09-09T00:41:12,985 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,985 37 | # define UNUSED(x) x 2025-09-09T00:41:12,985 | ^ 2025-09-09T00:41:12,985 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:41:12,985 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,985 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,986 | ^ 2025-09-09T00:41:12,986 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,986 37 | # define UNUSED(x) x 2025-09-09T00:41:12,986 | ^ 2025-09-09T00:41:12,986 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:41:12,986 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,986 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,987 | ^ 2025-09-09T00:41:12,987 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,987 37 | # define UNUSED(x) x 2025-09-09T00:41:12,987 | ^ 2025-09-09T00:41:12,987 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:41:12,987 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,987 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,987 | ^ 2025-09-09T00:41:12,987 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,988 37 | # define UNUSED(x) x 2025-09-09T00:41:12,988 | ^ 2025-09-09T00:41:12,988 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:41:12,988 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,988 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,988 | ^ 2025-09-09T00:41:12,988 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,988 37 | # define UNUSED(x) x 2025-09-09T00:41:12,989 | ^ 2025-09-09T00:41:12,989 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:41:12,989 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,989 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,989 | ^ 2025-09-09T00:41:12,989 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,989 37 | # define UNUSED(x) x 2025-09-09T00:41:12,990 | ^ 2025-09-09T00:41:12,990 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:41:12,990 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,990 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,990 | ^ 2025-09-09T00:41:12,990 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,990 37 | # define UNUSED(x) x 2025-09-09T00:41:12,990 | ^ 2025-09-09T00:41:12,991 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:41:12,991 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:41:12,991 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:41:12,991 | ^ 2025-09-09T00:41:12,991 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:12,991 37 | # define UNUSED(x) x 2025-09-09T00:41:12,991 | ^ 2025-09-09T00:41:13,723 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = true]’: 2025-09-09T00:41:13,723 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = true]’ 2025-09-09T00:41:13,723 470 | i->template Compute(); 2025-09-09T00:41:13,723 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:41:13,724 include/forcefields/forcefielduff.h:192:37: required from here 2025-09-09T00:41:13,724 192 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:41:13,724 | ~~~~~~~~~~~^~ 2025-09-09T00:41:13,724 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2025-09-09T00:41:13,724 423 | double ab[3]; 2025-09-09T00:41:13,724 | ^~ 2025-09-09T00:41:13,726 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = false]’: 2025-09-09T00:41:13,726 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = false]’ 2025-09-09T00:41:13,726 470 | i->template Compute(); 2025-09-09T00:41:13,726 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:41:13,726 include/forcefields/forcefielduff.h:192:54: required from here 2025-09-09T00:41:13,726 192 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:41:13,727 | ~~~~~~~~~~~~^~ 2025-09-09T00:41:13,727 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2025-09-09T00:41:13,727 423 | double ab[3]; 2025-09-09T00:41:13,727 | ^~ 2025-09-09T00:41:18,422 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:18,422 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:41:18,422 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:18,422 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:18,422 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:18,422 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:41:18,422 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:18,422 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:18,423 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,423 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:41:18,423 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:41:18,423 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:41:18,423 | ^~~~~~~ 2025-09-09T00:41:18,424 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:18,424 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:41:18,424 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:18,424 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:18,424 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:18,424 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:41:18,424 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:18,424 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:18,425 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,425 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:41:18,425 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:41:18,425 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:41:18,425 | ^~~~~~~ 2025-09-09T00:41:18,425 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:18,426 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:41:18,426 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:18,426 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:18,426 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:18,426 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:41:18,426 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:18,426 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:18,426 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,426 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:41:18,427 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:41:18,427 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:41:18,427 | ^~~~~~~ 2025-09-09T00:41:18,427 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’, 2025-09-09T00:41:18,427 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:18,427 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:18,427 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:18,427 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:41:18,428 include/forcefields/forcefielduff.h:82:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:18,428 82 | class OBFFElectrostaticCalculationUFF : public OBFFCalculation2 2025-09-09T00:41:18,428 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,428 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:41:18,428 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::rab’ was declared here 2025-09-09T00:41:18,428 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:41:18,428 | ^~~~~~~ 2025-09-09T00:41:18,429 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:18,429 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:41:18,429 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:18,429 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:18,429 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:41:18,429 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:41:18,429 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:41:18,430 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:18,430 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:18,430 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,430 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:41:18,430 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:41:18,430 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:41:18,430 | ^~~~~~~ 2025-09-09T00:41:18,430 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:18,430 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:41:18,431 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:18,431 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:18,431 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFElectrostaticCalculationUFF&}; _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:41:18,431 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFElectrostaticCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:41:18,431 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:41:18,431 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:18,431 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:18,431 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,431 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:41:18,431 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:41:18,432 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:41:18,432 | ^~~~~~~ 2025-09-09T00:41:18,920 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Bond() [with bool = true]’: 2025-09-09T00:41:18,920 ./src/forcefields/forcefielduff.cpp:93:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:18,920 93 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %4.2f%8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:41:18,920 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,920 94 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:18,920 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:18,920 95 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:41:18,920 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,072 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Bond() [with bool = false]’: 2025-09-09T00:41:19,072 ./src/forcefields/forcefielduff.cpp:93:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:19,072 93 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %4.2f%8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:41:19,072 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,072 94 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:19,072 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,072 95 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:41:19,072 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,207 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Angle() [with bool = false]’: 2025-09-09T00:41:19,207 ./src/forcefields/forcefielduff.cpp:220:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:19,207 220 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s%8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:19,207 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,207 221 | (*i).c->GetType(), (*i).theta * RAD_TO_DEG, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:41:19,207 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,515 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = false]’: 2025-09-09T00:41:19,515 ./src/forcefields/forcefielduff.cpp:479:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:19,515 479 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:19,515 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,515 480 | (*i).rab, (*i).kab, (*i).energy); 2025-09-09T00:41:19,515 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,672 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Electrostatic() [with bool = false]’: 2025-09-09T00:41:19,672 ./src/forcefields/forcefielduff.cpp:556:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:19,672 556 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:19,672 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,672 557 | (*i).rab, (*i).qq, (*i).energy); 2025-09-09T00:41:19,672 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,939 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Angle() [with bool = true]’: 2025-09-09T00:41:19,939 ./src/forcefields/forcefielduff.cpp:220:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:19,940 220 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s%8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:19,940 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:19,940 221 | (*i).c->GetType(), (*i).theta * RAD_TO_DEG, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:41:19,940 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,143 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Torsion() [with bool = true]’: 2025-09-09T00:41:20,143 ./src/forcefields/forcefielduff.cpp:307:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:20,144 307 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s %-5s%6.3f %8.3f %8.3f\n", 2025-09-09T00:41:20,144 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,144 308 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:20,144 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,144 309 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, 2025-09-09T00:41:20,144 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,144 310 | (*i).tor * RAD_TO_DEG, (*i).energy); 2025-09-09T00:41:20,144 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,357 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Torsion() [with bool = false]’: 2025-09-09T00:41:20,357 ./src/forcefields/forcefielduff.cpp:307:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:20,357 307 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s %-5s%6.3f %8.3f %8.3f\n", 2025-09-09T00:41:20,357 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,357 308 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:41:20,358 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,358 309 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, 2025-09-09T00:41:20,358 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,358 310 | (*i).tor * RAD_TO_DEG, (*i).energy); 2025-09-09T00:41:20,358 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,529 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_OOP() [with bool = true]’: 2025-09-09T00:41:20,529 ./src/forcefields/forcefielduff.cpp:389:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:20,529 389 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s %-5s%8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), (*i).c->GetType(), (*i).d->GetType(), 2025-09-09T00:41:20,529 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,529 390 | (*i).angle * RAD_TO_DEG, (*i).koop, (*i).energy); 2025-09-09T00:41:20,529 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,714 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_OOP() [with bool = false]’: 2025-09-09T00:41:20,714 ./src/forcefields/forcefielduff.cpp:389:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:20,715 389 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s %-5s%8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), (*i).c->GetType(), (*i).d->GetType(), 2025-09-09T00:41:20,715 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:20,715 390 | (*i).angle * RAD_TO_DEG, (*i).koop, (*i).energy); 2025-09-09T00:41:20,715 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,896 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:22,896 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:41:22,896 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,896 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,896 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,896 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:41:22,897 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,897 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:22,897 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,897 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,897 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:41:22,897 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:41:22,897 | ^~~~~~~~ 2025-09-09T00:41:22,898 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:22,898 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:41:22,898 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,898 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,899 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,899 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:41:22,899 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,899 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:22,899 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,899 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,899 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:41:22,899 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:41:22,899 | ^~~~~~~~ 2025-09-09T00:41:22,900 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:22,900 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:41:22,900 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,901 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,901 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,901 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:41:22,901 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,901 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:22,901 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,901 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,901 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:41:22,901 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:41:22,901 | ^~~~~~~~ 2025-09-09T00:41:22,902 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2025-09-09T00:41:22,902 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,902 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,902 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,902 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:41:22,902 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,902 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2025-09-09T00:41:22,902 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,903 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,903 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::rab’ was declared here 2025-09-09T00:41:22,903 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:41:22,903 | ^~~~~~~~ 2025-09-09T00:41:22,903 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2025-09-09T00:41:22,903 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,903 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,904 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,904 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:41:22,904 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,904 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2025-09-09T00:41:22,904 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,904 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,904 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::delta’ was declared here 2025-09-09T00:41:22,904 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:41:22,904 | ^~~~~~~~ 2025-09-09T00:41:22,905 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:22,905 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:41:22,906 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,906 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,906 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:41:22,906 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:41:22,906 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:41:22,906 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,906 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:22,906 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,906 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,907 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:41:22,907 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:41:22,907 | ^~~~~~~~ 2025-09-09T00:41:22,907 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:22,908 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:41:22,908 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++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,908 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++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,908 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFBondCalculationUFF&}; _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:41:22,908 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFBondCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:41:22,908 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:41:22,908 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,908 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:22,908 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,910 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,910 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:41:22,910 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:41:22,910 | ^~~~~~~~ 2025-09-09T00:41:22,914 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:41:22,914 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:41:22,914 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’ at include/forcefields/forcefielduff.h:39:9, 2025-09-09T00:41:22,914 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,914 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,914 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,914 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,914 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,915 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:41:22,915 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,915 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,915 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:41:22,915 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,915 | ^~~~~~~~~ 2025-09-09T00:41:22,915 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,915 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,915 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,915 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,916 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,916 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::at’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,916 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,916 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,916 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,916 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::at’ was declared here 2025-09-09T00:41:22,916 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,916 | ^~~~~~~~~ 2025-09-09T00:41:22,916 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,916 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,917 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,917 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,917 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,917 include/forcefields/forcefielduff.h:39:9: warning: ‘*(unsigned char*)((char*)&anglecalc + offsetof(OpenBabel::OBFFAngleCalculationUFF, OpenBabel::OBFFAngleCalculationUFF::linear))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,917 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,917 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,917 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,917 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘*(unsigned char*)((char*)&anglecalc + offsetof(OpenBabel::OBFFAngleCalculationUFF, OpenBabel::OBFFAngleCalculationUFF::linear))’ was declared here 2025-09-09T00:41:22,917 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,917 | ^~~~~~~~~ 2025-09-09T00:41:22,917 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,918 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,918 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,918 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,918 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,918 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,918 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,918 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,918 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,918 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::theta’ was declared here 2025-09-09T00:41:22,918 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,919 | ^~~~~~~~~ 2025-09-09T00:41:22,919 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,919 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,919 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,919 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,919 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,919 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,919 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,919 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,920 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,920 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::delta’ was declared here 2025-09-09T00:41:22,920 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,920 | ^~~~~~~~~ 2025-09-09T00:41:22,920 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,920 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,920 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,920 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,921 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,921 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rij’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,921 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,921 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,921 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,921 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rij’ was declared here 2025-09-09T00:41:22,921 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,921 | ^~~~~~~~~ 2025-09-09T00:41:22,921 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,922 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,922 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,922 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,922 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,922 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rjk’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,922 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,922 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,922 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,922 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rjk’ was declared here 2025-09-09T00:41:22,922 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,922 | ^~~~~~~~~ 2025-09-09T00:41:22,923 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,923 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,923 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,923 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1288:30, 2025-09-09T00:41:22,923 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,923 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rik’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,923 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,923 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,923 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,924 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rik’ was declared here 2025-09-09T00:41:22,924 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,924 | ^~~~~~~~~ 2025-09-09T00:41:22,924 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:41:22,924 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:41:22,924 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationUFF; _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:41:22,924 inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const OpenBabel::OBFFAngleCalculationUFF&}; _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:634:26, 2025-09-09T00:41:22,925 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBFFAngleCalculationUFF; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1294:21, 2025-09-09T00:41:22,925 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:41:22,925 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::n’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:22,925 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:41:22,925 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:22,925 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:41:22,925 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::n’ was declared here 2025-09-09T00:41:22,925 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:41:22,925 | ^~~~~~~~~ 2025-09-09T00:41:30,227 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetTypes()’: 2025-09-09T00:41:30,227 ./src/forcefields/forcefielduff.cpp:1708:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:41:30,227 1708 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:41:30,228 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:30,228 1709 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:41:30,228 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:31,933 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefielduff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/' 2025-09-09T00:41:31,934 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/forcefields/forcefielduff.o /tmp/cc81jEZH.s 2025-09-09T00:41:31,941 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:33,259 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:41:33,259 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:41:33,259 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefielduff.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/forcefields/forcefielduff.' 2025-09-09T00:41:33,263 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/format.cpp -o build/temp.linux-armv7l-cpython-313/src/format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:41:33,268 Using built-in specs. 2025-09-09T00:41:33,269 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:33,269 Target: arm-linux-gnueabihf 2025-09-09T00:41:33,269 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:41:33,269 Thread model: posix 2025-09-09T00:41:33,270 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:33,270 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:33,270 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:41:33,270 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/format.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/ -dumpbase format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccRAyYlI.s 2025-09-09T00:41:33,281 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:33,281 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:41:33,281 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:33,281 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:33,282 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:33,282 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:33,283 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:33,283 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:33,283 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:33,283 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:33,283 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:33,283 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:33,284 #include "..." search starts here: 2025-09-09T00:41:33,284 #include <...> search starts here: 2025-09-09T00:41:33,284 /usr/include/eigen3 2025-09-09T00:41:33,284 include 2025-09-09T00:41:33,284 /usr/include/python3.13 2025-09-09T00:41:33,284 /usr/include/c++/14 2025-09-09T00:41:33,284 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:33,284 /usr/include/c++/14/backward 2025-09-09T00:41:33,285 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:33,285 /usr/local/include 2025-09-09T00:41:33,285 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:33,285 /usr/include 2025-09-09T00:41:33,285 End of search list. 2025-09-09T00:41:33,301 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:34,461 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:34,462 from ./src/format.cpp:20: 2025-09-09T00:41:34,462 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:34,462 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:34,462 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:34,462 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:41:34,462 from include/openbabel/plugin.h:23: 2025-09-09T00:41:34,462 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:34,462 131 | struct binary_function 2025-09-09T00:41:34,463 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:35,664 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/' 2025-09-09T00:41:35,664 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/format.o /tmp/ccRAyYlI.s 2025-09-09T00:41:35,669 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:35,781 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:41:35,781 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:41:35,781 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/format.' 2025-09-09T00:41:35,782 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/APIInterface.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/APIInterface.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:41:35,786 Using built-in specs. 2025-09-09T00:41:35,787 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:35,787 Target: arm-linux-gnueabihf 2025-09-09T00:41:35,787 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:41:35,787 Thread model: posix 2025-09-09T00:41:35,787 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:35,787 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:35,787 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/APIInterface.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:41:35,788 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/APIInterface.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase APIInterface.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc0umRSx.s 2025-09-09T00:41:35,799 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:35,799 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:41:35,799 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:35,799 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:35,799 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:35,800 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:35,800 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:35,800 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:35,800 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:35,800 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:35,800 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:35,800 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:35,801 #include "..." search starts here: 2025-09-09T00:41:35,801 #include <...> search starts here: 2025-09-09T00:41:35,801 /usr/include/eigen3 2025-09-09T00:41:35,801 include 2025-09-09T00:41:35,801 /usr/include/python3.13 2025-09-09T00:41:35,801 /usr/include/c++/14 2025-09-09T00:41:35,801 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:35,801 /usr/include/c++/14/backward 2025-09-09T00:41:35,801 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:35,802 /usr/local/include 2025-09-09T00:41:35,802 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:35,802 /usr/include 2025-09-09T00:41:35,802 End of search list. 2025-09-09T00:41:35,816 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:37,145 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:37,146 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:37,146 from ./src/formats/APIInterface.cpp:19: 2025-09-09T00:41:37,146 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:37,146 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:37,146 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:37,146 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:41:37,146 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:41:37,146 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:41:37,146 from /usr/include/c++/14/ios:44, 2025-09-09T00:41:37,147 from /usr/include/c++/14/ostream:40, 2025-09-09T00:41:37,147 from /usr/include/c++/14/iostream:41, 2025-09-09T00:41:37,147 from include/openbabel/obconversion.h:24: 2025-09-09T00:41:37,147 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:37,147 131 | struct binary_function 2025-09-09T00:41:37,147 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:38,032 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/APIInterface.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:41:38,032 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/APIInterface.o /tmp/cc0umRSx.s 2025-09-09T00:41:38,037 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:38,131 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:41:38,132 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:41:38,132 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/APIInterface.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/APIInterface.' 2025-09-09T00:41:38,133 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/ArrayList.c -o build/temp.linux-armv7l-cpython-313/src/formats/ArrayList.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:41:38,137 Using built-in specs. 2025-09-09T00:41:38,138 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-09T00:41:38,138 Target: arm-linux-gnueabihf 2025-09-09T00:41:38,138 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:41:38,138 Thread model: posix 2025-09-09T00:41:38,138 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:38,138 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:38,138 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/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-313/src/formats/' 2025-09-09T00:41:38,138 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1 -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D NDEBUG ./src/formats/ArrayList.c -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase ArrayList.c -dumpbase-ext .c -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccgDJMb1.s 2025-09-09T00:41:38,147 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 2025-09-09T00:41:38,148 GNU C17 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:38,148 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:41:38,148 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:38,148 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:38,148 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:38,148 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:38,149 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:38,149 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:38,149 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:38,149 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:38,149 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:38,149 #include "..." search starts here: 2025-09-09T00:41:38,149 #include <...> search starts here: 2025-09-09T00:41:38,149 /usr/include/eigen3 2025-09-09T00:41:38,149 include 2025-09-09T00:41:38,149 /usr/include/python3.13 2025-09-09T00:41:38,149 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:38,150 /usr/local/include 2025-09-09T00:41:38,150 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:38,150 /usr/include 2025-09-09T00:41:38,150 End of search list. 2025-09-09T00:41:38,162 Compiler executable checksum: 04388919d42652114d16308b030ced8f 2025-09-09T00:41:38,375 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/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-313/src/formats/' 2025-09-09T00:41:38,375 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/ArrayList.o /tmp/ccgDJMb1.s 2025-09-09T00:41:38,380 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:38,390 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:41:38,390 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:41:38,391 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/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-313/src/formats/ArrayList.' 2025-09-09T00:41:38,392 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/CSRformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/CSRformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:41:38,396 Using built-in specs. 2025-09-09T00:41:38,397 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:38,397 Target: arm-linux-gnueabihf 2025-09-09T00:41:38,397 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:41:38,397 Thread model: posix 2025-09-09T00:41:38,397 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:38,397 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:38,398 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/CSRformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:41:38,398 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/CSRformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase CSRformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccGP8Yg3.s 2025-09-09T00:41:38,410 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:38,411 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:41:38,411 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:38,411 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:38,411 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:38,411 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:38,412 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:38,412 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:38,412 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:38,412 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:38,412 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:38,412 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:38,412 #include "..." search starts here: 2025-09-09T00:41:38,413 #include <...> search starts here: 2025-09-09T00:41:38,413 /usr/include/eigen3 2025-09-09T00:41:38,413 include 2025-09-09T00:41:38,413 /usr/include/python3.13 2025-09-09T00:41:38,413 /usr/include/c++/14 2025-09-09T00:41:38,413 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:38,413 /usr/include/c++/14/backward 2025-09-09T00:41:38,414 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:38,414 /usr/local/include 2025-09-09T00:41:38,414 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:38,414 /usr/include 2025-09-09T00:41:38,414 End of search list. 2025-09-09T00:41:38,429 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:39,936 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:39,937 from include/openbabel/mol.h:43, 2025-09-09T00:41:39,937 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:39,937 from ./src/formats/CSRformat.cpp:17: 2025-09-09T00:41:39,937 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:39,937 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:39,937 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:39,937 | ^ 2025-09-09T00:41:39,937 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:39,937 37 | # define UNUSED(x) x 2025-09-09T00:41:39,938 | ^ 2025-09-09T00:41:40,550 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:40,550 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:40,550 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:40,550 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:40,550 | ^ 2025-09-09T00:41:40,550 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:40,550 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:40,550 | ^~~~~~~~ 2025-09-09T00:41:40,553 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:40,554 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:40,554 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:40,554 | ^ 2025-09-09T00:41:40,554 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:40,554 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:40,554 | ^~~~~~~~ 2025-09-09T00:41:40,568 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:40,568 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:40,568 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:40,568 | ^ 2025-09-09T00:41:40,568 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:40,568 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:40,568 | ^~~~~~~~ 2025-09-09T00:41:40,573 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:40,573 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:40,573 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:40,573 | ^ 2025-09-09T00:41:40,573 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:40,573 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:40,573 | ^~~~~~~~ 2025-09-09T00:41:40,711 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:40,712 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:40,712 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:40,712 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:40,712 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:40,712 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:40,712 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:40,712 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:40,712 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:40,712 from include/openbabel/mol.h:35: 2025-09-09T00:41:40,713 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:40,713 131 | struct binary_function 2025-09-09T00:41:40,713 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:42,540 ./src/formats/CSRformat.cpp: In member function ‘char* OpenBabel::CSRFormat::PadString(char*, int)’: 2025-09-09T00:41:42,540 ./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] 2025-09-09T00:41:42,540 188 | strncpy(output, input, strlen(input)); 2025-09-09T00:41:42,540 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:42,540 ./src/formats/CSRformat.cpp:188:12: note: length computed here 2025-09-09T00:41:42,540 188 | strncpy(output, input, strlen(input)); 2025-09-09T00:41:42,540 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:42,720 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/CSRformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:41:42,721 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/CSRformat.o /tmp/ccGP8Yg3.s 2025-09-09T00:41:42,727 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:42,883 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:41:42,884 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:41:42,884 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/CSRformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/CSRformat.' 2025-09-09T00:41:42,886 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/MCDLformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/MCDLformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:41:42,890 Using built-in specs. 2025-09-09T00:41:42,891 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:42,891 Target: arm-linux-gnueabihf 2025-09-09T00:41:42,891 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:41:42,892 Thread model: posix 2025-09-09T00:41:42,892 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:42,892 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:42,892 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/MCDLformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:41:42,894 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/MCDLformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase MCDLformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccjjewqm.s 2025-09-09T00:41:42,906 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:42,906 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:41:42,907 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:42,907 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:42,908 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:42,908 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:42,908 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:42,909 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:42,909 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:42,909 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:42,909 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:42,910 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:42,910 #include "..." search starts here: 2025-09-09T00:41:42,910 #include <...> search starts here: 2025-09-09T00:41:42,910 /usr/include/eigen3 2025-09-09T00:41:42,911 include 2025-09-09T00:41:42,911 /usr/include/python3.13 2025-09-09T00:41:42,911 /usr/include/c++/14 2025-09-09T00:41:42,911 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:42,911 /usr/include/c++/14/backward 2025-09-09T00:41:42,912 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:42,912 /usr/local/include 2025-09-09T00:41:42,912 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:42,912 /usr/include 2025-09-09T00:41:42,912 End of search list. 2025-09-09T00:41:42,935 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:44,450 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:44,450 from include/openbabel/mol.h:43, 2025-09-09T00:41:44,450 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:44,450 from ./src/formats/MCDLformat.cpp:21: 2025-09-09T00:41:44,450 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:44,450 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:44,450 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:44,450 | ^ 2025-09-09T00:41:44,450 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:44,450 37 | # define UNUSED(x) x 2025-09-09T00:41:44,451 | ^ 2025-09-09T00:41:45,064 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:45,064 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:45,064 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:45,064 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:45,065 | ^ 2025-09-09T00:41:45,065 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:45,065 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:45,065 | ^~~~~~~~ 2025-09-09T00:41:45,069 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:45,069 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:45,069 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:45,069 | ^ 2025-09-09T00:41:45,070 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:45,070 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:45,070 | ^~~~~~~~ 2025-09-09T00:41:45,084 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:45,085 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:45,085 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:45,085 | ^ 2025-09-09T00:41:45,085 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:45,085 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:45,085 | ^~~~~~~~ 2025-09-09T00:41:45,090 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:45,091 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:45,091 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:45,091 | ^ 2025-09-09T00:41:45,091 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:45,091 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:45,091 | ^~~~~~~~ 2025-09-09T00:41:45,230 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:45,230 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:45,231 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:45,231 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:45,231 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:45,231 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:45,231 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:45,232 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:45,232 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:45,232 from include/openbabel/mol.h:35: 2025-09-09T00:41:45,232 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:45,232 131 | struct binary_function 2025-09-09T00:41:45,232 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:45,406 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::constring(int (*)[4], char*)’: 2025-09-09T00:41:45,407 ./src/formats/MCDLformat.cpp:174:66: warning: unused parameter ‘tstr’ [-Wunused-parameter] 2025-09-09T00:41:45,407 174 | string MCDLFormat::constring(int conntab [MAXBONDS][4], char * tstr) 2025-09-09T00:41:45,407 | ~~~~~~~^~~~ 2025-09-09T00:41:45,409 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2025-09-09T00:41:45,410 ./src/formats/MCDLformat.cpp:278:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:41:45,410 278 | if (jflag) 2025-09-09T00:41:45,410 | ^~ 2025-09-09T00:41:45,410 ./src/formats/MCDLformat.cpp:282:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:41:45,410 282 | nt = 1; 2025-09-09T00:41:45,410 | ^~ 2025-09-09T00:41:45,452 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::getMCDL(OpenBabel::OBMol*, bool)’: 2025-09-09T00:41:45,452 ./src/formats/MCDLformat.cpp:529:10: warning: variable ‘test’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:41:45,453 529 | bool test;//, testParity; 2025-09-09T00:41:45,453 | ^~~~ 2025-09-09T00:41:45,458 ./src/formats/MCDLformat.cpp:479:48: warning: unused parameter ‘includeCoordinates’ [-Wunused-parameter] 2025-09-09T00:41:45,458 479 | string MCDLFormat::getMCDL(OBMol* pmol, bool includeCoordinates) { 2025-09-09T00:41:45,458 | ~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:45,460 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::restoreFullMCDL(std::string, OpenBabel::OBMol*)’: 2025-09-09T00:41:45,460 ./src/formats/MCDLformat.cpp:948:43: warning: unused parameter ‘value’ [-Wunused-parameter] 2025-09-09T00:41:45,461 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2025-09-09T00:41:45,461 | ~~~~~~~^~~~~ 2025-09-09T00:41:45,461 ./src/formats/MCDLformat.cpp:948:57: warning: unused parameter ‘pmol’ [-Wunused-parameter] 2025-09-09T00:41:45,461 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2025-09-09T00:41:45,461 | ~~~~~~~^~~~ 2025-09-09T00:41:45,471 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::setMCDL(std::string, OpenBabel::OBMol*, std::string&)’: 2025-09-09T00:41:45,471 ./src/formats/MCDLformat.cpp:1031:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:41:45,471 1031 | if (n1 < 0) n1=indexOf(s,"-"); 2025-09-09T00:41:45,471 | ~~~^~~ 2025-09-09T00:41:45,478 ./src/formats/MCDLformat.cpp:1032:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:41:45,478 1032 | if (n1 < 0) n1=indexOf(s,"*"); 2025-09-09T00:41:45,478 | ~~~^~~ 2025-09-09T00:41:45,479 ./src/formats/MCDLformat.cpp:1033:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:41:45,479 1033 | if (n1 < 0) { 2025-09-09T00:41:45,479 | ~~~^~~ 2025-09-09T00:41:45,481 ./src/formats/MCDLformat.cpp:1062:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,482 1062 | if (n1>=0) { 2025-09-09T00:41:45,482 | ~~^~~ 2025-09-09T00:41:45,483 ./src/formats/MCDLformat.cpp:1070:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,483 1070 | if (n1>=0) { 2025-09-09T00:41:45,484 | ~~^~~ 2025-09-09T00:41:45,485 ./src/formats/MCDLformat.cpp:1079:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,485 1079 | if (n1>=0) { 2025-09-09T00:41:45,486 | ~~^~~ 2025-09-09T00:41:45,489 ./src/formats/MCDLformat.cpp:1092:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,489 1092 | if (n1>=0) { 2025-09-09T00:41:45,489 | ~~^~~ 2025-09-09T00:41:45,492 ./src/formats/MCDLformat.cpp:1118:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:41:45,493 1118 | if (n1<0) { 2025-09-09T00:41:45,493 | ~~^~ 2025-09-09T00:41:45,493 ./src/formats/MCDLformat.cpp:1121:25: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,493 1121 | if ((n2=0)) n1=n2; 2025-09-09T00:41:45,493 | ~~^~~ 2025-09-09T00:41:45,505 ./src/formats/MCDLformat.cpp:1266:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:41:45,505 1266 | if (nPrev == acount) { 2025-09-09T00:41:45,505 | ~~~~~~^~~~~~~~~ 2025-09-09T00:41:45,508 ./src/formats/MCDLformat.cpp:1298:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:41:45,508 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2025-09-09T00:41:45,508 | ~~^~ 2025-09-09T00:41:45,508 ./src/formats/MCDLformat.cpp:1298:45: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,509 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2025-09-09T00:41:45,509 | ~~^~~ 2025-09-09T00:41:45,509 ./src/formats/MCDLformat.cpp:1300:12: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,509 1300 | if ((n1>=0) && (value.length() > n1)) { 2025-09-09T00:41:45,509 | ~~^~~ 2025-09-09T00:41:45,510 ./src/formats/MCDLformat.cpp:1312:13: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,511 1312 | if (n1>=0) { 2025-09-09T00:41:45,511 | ~~^~~ 2025-09-09T00:41:45,523 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::indexOf(std::string, std::string, int)’: 2025-09-09T00:41:45,523 ./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] 2025-09-09T00:41:45,523 1384 | if (result == string::npos) result=-1; 2025-09-09T00:41:45,523 | ~~~~~~~^~~~~~~~~~~~~~~ 2025-09-09T00:41:45,523 ./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] 2025-09-09T00:41:45,524 1385 | if (result >= instring.length()) result=-1; 2025-09-09T00:41:45,524 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:45,525 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::lastIndexOf(std::string, std::string)’: 2025-09-09T00:41:45,525 ./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] 2025-09-09T00:41:45,525 1398 | if (n == string::npos) 2025-09-09T00:41:45,525 | ~~^~~~~~~~~~~~~~~ 2025-09-09T00:41:45,527 ./src/formats/MCDLformat.cpp: In member function ‘bool OpenBabel::MCDLFormat::parseFormula(std::string, std::vector&)’: 2025-09-09T00:41:45,527 ./src/formats/MCDLformat.cpp:1426:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,527 1426 | if (n>=0) { 2025-09-09T00:41:45,527 | ~^~~ 2025-09-09T00:41:45,530 ./src/formats/MCDLformat.cpp:1449:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:41:45,530 1449 | if (n>=0) { 2025-09-09T00:41:45,530 | ~^~~ 2025-09-09T00:41:49,424 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2025-09-09T00:41:49,424 ./src/formats/MCDLformat.cpp:385:24: warning: ‘numdups’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:49,424 385 | for (j=0; j dupfrag) 2025-09-09T00:41:49,426 | ^~ 2025-09-09T00:41:49,427 ./src/formats/MCDLformat.cpp:237:19: note: ‘dupfrag’ was declared here 2025-09-09T00:41:49,427 237 | int numdups, dupfrag, jump; 2025-09-09T00:41:49,427 | ^~~~~~~ 2025-09-09T00:41:49,427 ./src/formats/MCDLformat.cpp:398:35: warning: ‘jump’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:49,427 398 | ix[i] = mx[i] + jump + 1; 2025-09-09T00:41:49,427 | ~~~~~~^~~~~~ 2025-09-09T00:41:49,428 ./src/formats/MCDLformat.cpp:237:28: note: ‘jump’ was declared here 2025-09-09T00:41:49,428 237 | int numdups, dupfrag, jump; 2025-09-09T00:41:49,428 | ^~~~ 2025-09-09T00:42:01,418 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/MCDLformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:01,418 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/MCDLformat.o /tmp/ccjjewqm.s 2025-09-09T00:42:01,423 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:02,767 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:02,767 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:02,767 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/MCDLformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/MCDLformat.' 2025-09-09T00:42:02,767 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/MNAformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/MNAformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:02,771 Using built-in specs. 2025-09-09T00:42:02,773 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:02,773 Target: arm-linux-gnueabihf 2025-09-09T00:42:02,773 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:02,773 Thread model: posix 2025-09-09T00:42:02,773 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:02,774 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:02,774 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/MNAformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:02,776 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/MNAformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase MNAformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccmLHZqy.s 2025-09-09T00:42:02,788 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:02,788 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:02,789 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:02,789 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:02,790 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:02,790 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:02,791 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:02,791 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:02,791 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:02,791 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:02,792 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:02,792 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:02,792 #include "..." search starts here: 2025-09-09T00:42:02,792 #include <...> search starts here: 2025-09-09T00:42:02,792 /usr/include/eigen3 2025-09-09T00:42:02,793 include 2025-09-09T00:42:02,793 /usr/include/python3.13 2025-09-09T00:42:02,793 /usr/include/c++/14 2025-09-09T00:42:02,793 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:02,793 /usr/include/c++/14/backward 2025-09-09T00:42:02,794 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:02,794 /usr/local/include 2025-09-09T00:42:02,794 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:02,794 /usr/include 2025-09-09T00:42:02,794 End of search list. 2025-09-09T00:42:02,813 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:04,326 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:04,326 from include/openbabel/mol.h:43, 2025-09-09T00:42:04,326 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:04,326 from ./src/formats/MNAformat.cpp:31: 2025-09-09T00:42:04,327 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:04,327 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:04,327 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:04,327 | ^ 2025-09-09T00:42:04,327 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:04,327 37 | # define UNUSED(x) x 2025-09-09T00:42:04,327 | ^ 2025-09-09T00:42:04,939 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:04,940 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:04,940 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:04,940 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:04,940 | ^ 2025-09-09T00:42:04,940 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:04,940 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:04,940 | ^~~~~~~~ 2025-09-09T00:42:04,944 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:04,944 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:04,945 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:04,945 | ^ 2025-09-09T00:42:04,945 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:04,945 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:04,945 | ^~~~~~~~ 2025-09-09T00:42:04,960 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:04,960 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:04,960 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:04,960 | ^ 2025-09-09T00:42:04,960 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:04,960 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:04,960 | ^~~~~~~~ 2025-09-09T00:42:04,966 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:04,966 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:04,966 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:04,966 | ^ 2025-09-09T00:42:04,966 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:04,966 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:04,966 | ^~~~~~~~ 2025-09-09T00:42:05,105 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:05,105 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:05,105 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:05,106 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:05,106 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:05,106 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:05,106 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:05,107 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:05,107 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:05,107 from include/openbabel/mol.h:35: 2025-09-09T00:42:05,107 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:05,107 131 | struct binary_function 2025-09-09T00:42:05,107 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:08,716 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/MNAformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:08,717 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/MNAformat.o /tmp/ccmLHZqy.s 2025-09-09T00:42:08,722 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:09,046 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:09,047 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:09,047 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/MNAformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/MNAformat.' 2025-09-09T00:42:09,049 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/PQSformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/PQSformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:09,053 Using built-in specs. 2025-09-09T00:42:09,054 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:09,054 Target: arm-linux-gnueabihf 2025-09-09T00:42:09,054 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:09,054 Thread model: posix 2025-09-09T00:42:09,054 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:09,054 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:09,054 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/PQSformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:09,055 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/PQSformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase PQSformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccrFiAsq.s 2025-09-09T00:42:09,065 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:09,066 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:09,066 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:09,066 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:09,066 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:09,067 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:09,067 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:09,067 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:09,067 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:09,067 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:09,067 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:09,067 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:09,068 #include "..." search starts here: 2025-09-09T00:42:09,068 #include <...> search starts here: 2025-09-09T00:42:09,068 /usr/include/eigen3 2025-09-09T00:42:09,068 include 2025-09-09T00:42:09,068 /usr/include/python3.13 2025-09-09T00:42:09,068 /usr/include/c++/14 2025-09-09T00:42:09,068 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:09,069 /usr/include/c++/14/backward 2025-09-09T00:42:09,069 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:09,069 /usr/local/include 2025-09-09T00:42:09,069 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:09,069 /usr/include 2025-09-09T00:42:09,069 End of search list. 2025-09-09T00:42:09,085 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:10,603 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:10,603 from include/openbabel/mol.h:43, 2025-09-09T00:42:10,603 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:10,603 from ./src/formats/PQSformat.cpp:16: 2025-09-09T00:42:10,603 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:10,603 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:10,604 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:10,604 | ^ 2025-09-09T00:42:10,604 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:10,604 37 | # define UNUSED(x) x 2025-09-09T00:42:10,604 | ^ 2025-09-09T00:42:11,214 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:11,214 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:11,215 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:11,215 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:11,215 | ^ 2025-09-09T00:42:11,215 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:11,215 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:11,215 | ^~~~~~~~ 2025-09-09T00:42:11,218 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:11,218 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:11,218 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:11,218 | ^ 2025-09-09T00:42:11,219 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:11,219 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:11,219 | ^~~~~~~~ 2025-09-09T00:42:11,232 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:11,233 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:11,233 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:11,233 | ^ 2025-09-09T00:42:11,233 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:11,233 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:11,233 | ^~~~~~~~ 2025-09-09T00:42:11,237 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:11,238 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:11,238 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:11,238 | ^ 2025-09-09T00:42:11,238 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:11,238 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:11,238 | ^~~~~~~~ 2025-09-09T00:42:11,377 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:11,377 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:11,377 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:11,377 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:11,377 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:11,378 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:11,378 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:11,378 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:11,378 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:11,378 from include/openbabel/mol.h:35: 2025-09-09T00:42:11,378 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:11,378 131 | struct binary_function 2025-09-09T00:42:11,378 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:13,810 ./src/formats/PQSformat.cpp: In member function ‘virtual bool OpenBabel::PQSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:13,810 ./src/formats/PQSformat.cpp:259:49: warning: ‘pFormat’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:42:13,810 259 | return pFormat->ReadMolecule(&mol,&coordconv); 2025-09-09T00:42:13,810 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:42:13,810 ./src/formats/PQSformat.cpp:250:31: note: ‘pFormat’ was declared here 2025-09-09T00:42:13,810 250 | OBFormat* pFormat; 2025-09-09T00:42:13,810 | ^~~~~~~ 2025-09-09T00:42:14,418 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/PQSformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:14,419 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/PQSformat.o /tmp/ccrFiAsq.s 2025-09-09T00:42:14,430 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:14,671 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:14,671 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:14,671 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/PQSformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/PQSformat.' 2025-09-09T00:42:14,671 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/abinitformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/abinitformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:14,677 Using built-in specs. 2025-09-09T00:42:14,677 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:14,678 Target: arm-linux-gnueabihf 2025-09-09T00:42:14,678 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:14,678 Thread model: posix 2025-09-09T00:42:14,678 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:14,678 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:14,678 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/abinitformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:14,678 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/abinitformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase abinitformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccvkCfwP.s 2025-09-09T00:42:14,689 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:14,689 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:14,689 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:14,689 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:14,689 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:14,689 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:14,689 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:14,690 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:14,690 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:14,690 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:14,690 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:14,690 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:14,690 #include "..." search starts here: 2025-09-09T00:42:14,690 #include <...> search starts here: 2025-09-09T00:42:14,690 /usr/include/eigen3 2025-09-09T00:42:14,690 include 2025-09-09T00:42:14,691 /usr/include/python3.13 2025-09-09T00:42:14,691 /usr/include/c++/14 2025-09-09T00:42:14,691 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:14,691 /usr/include/c++/14/backward 2025-09-09T00:42:14,691 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:14,691 /usr/local/include 2025-09-09T00:42:14,691 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:14,691 /usr/include 2025-09-09T00:42:14,691 End of search list. 2025-09-09T00:42:14,708 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:16,213 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:16,214 from include/openbabel/mol.h:43, 2025-09-09T00:42:16,214 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:16,214 from ./src/formats/abinitformat.cpp:16: 2025-09-09T00:42:16,214 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:16,214 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:16,214 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:16,214 | ^ 2025-09-09T00:42:16,214 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:16,214 37 | # define UNUSED(x) x 2025-09-09T00:42:16,215 | ^ 2025-09-09T00:42:16,826 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:16,826 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:16,826 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:16,826 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:16,827 | ^ 2025-09-09T00:42:16,827 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:16,827 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:16,827 | ^~~~~~~~ 2025-09-09T00:42:16,830 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:16,830 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:16,830 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:16,830 | ^ 2025-09-09T00:42:16,830 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:16,830 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:16,831 | ^~~~~~~~ 2025-09-09T00:42:16,844 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:16,844 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:16,845 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:16,845 | ^ 2025-09-09T00:42:16,845 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:16,845 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:16,845 | ^~~~~~~~ 2025-09-09T00:42:16,849 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:16,850 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:16,850 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:16,850 | ^ 2025-09-09T00:42:16,850 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:16,850 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:16,850 | ^~~~~~~~ 2025-09-09T00:42:16,988 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:16,988 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:16,988 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:16,988 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:16,989 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:16,989 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:16,989 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:16,989 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:16,989 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:16,989 from include/openbabel/mol.h:35: 2025-09-09T00:42:16,989 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:16,989 131 | struct binary_function 2025-09-09T00:42:16,989 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:17,172 ./src/formats/abinitformat.cpp: In member function ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:17,172 ./src/formats/abinitformat.cpp:91:12: warning: variable ‘acell’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:42:17,173 91 | double acell[3]; // scale of lattice vectors 2025-09-09T00:42:17,173 | ^~~~~ 2025-09-09T00:42:19,469 ./src/formats/abinitformat.cpp:204:23: warning: ‘natom’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:42:19,469 204 | for (int i = 0; i < natom; ++i) { 2025-09-09T00:42:19,470 | ~~^~~~~~~ 2025-09-09T00:42:19,470 ./src/formats/abinitformat.cpp:82:9: note: ‘natom’ was declared here 2025-09-09T00:42:19,470 82 | int natom; 2025-09-09T00:42:19,470 | ^~~~~ 2025-09-09T00:42:20,080 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/abinitformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:20,080 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/abinitformat.o /tmp/ccvkCfwP.s 2025-09-09T00:42:20,085 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:20,344 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:20,344 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:20,344 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/abinitformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/abinitformat.' 2025-09-09T00:42:20,344 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/acesformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/acesformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:20,348 Using built-in specs. 2025-09-09T00:42:20,349 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:20,349 Target: arm-linux-gnueabihf 2025-09-09T00:42:20,349 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:20,350 Thread model: posix 2025-09-09T00:42:20,350 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:20,350 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:20,350 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/acesformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:20,350 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/acesformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase acesformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccdP8LuY.s 2025-09-09T00:42:20,360 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:20,360 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:20,360 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:20,360 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:20,360 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:20,361 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:20,361 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:20,361 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:20,361 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:20,361 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:20,361 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:20,361 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:20,361 #include "..." search starts here: 2025-09-09T00:42:20,361 #include <...> search starts here: 2025-09-09T00:42:20,362 /usr/include/eigen3 2025-09-09T00:42:20,362 include 2025-09-09T00:42:20,362 /usr/include/python3.13 2025-09-09T00:42:20,362 /usr/include/c++/14 2025-09-09T00:42:20,362 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:20,362 /usr/include/c++/14/backward 2025-09-09T00:42:20,362 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:20,362 /usr/local/include 2025-09-09T00:42:20,363 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:20,363 /usr/include 2025-09-09T00:42:20,363 End of search list. 2025-09-09T00:42:20,379 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:21,885 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:21,885 from include/openbabel/mol.h:43, 2025-09-09T00:42:21,885 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:21,885 from ./src/formats/acesformat.cpp:20: 2025-09-09T00:42:21,886 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:21,886 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:21,886 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:21,886 | ^ 2025-09-09T00:42:21,886 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:21,886 37 | # define UNUSED(x) x 2025-09-09T00:42:21,886 | ^ 2025-09-09T00:42:22,499 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:22,499 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:22,499 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:22,499 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:22,499 | ^ 2025-09-09T00:42:22,499 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:22,499 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:22,499 | ^~~~~~~~ 2025-09-09T00:42:22,502 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:22,503 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:22,503 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:22,503 | ^ 2025-09-09T00:42:22,503 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:22,503 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:22,503 | ^~~~~~~~ 2025-09-09T00:42:22,517 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:22,517 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:22,517 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:22,517 | ^ 2025-09-09T00:42:22,517 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:22,518 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:22,518 | ^~~~~~~~ 2025-09-09T00:42:22,522 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:22,522 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:22,522 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:22,522 | ^ 2025-09-09T00:42:22,522 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:22,523 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:22,523 | ^~~~~~~~ 2025-09-09T00:42:22,661 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:22,661 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:22,661 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:22,661 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:22,661 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:22,661 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:22,661 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:22,662 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:22,662 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:22,662 from include/openbabel/mol.h:35: 2025-09-09T00:42:22,662 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:22,662 131 | struct binary_function 2025-09-09T00:42:22,662 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:26,989 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/acesformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:26,990 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/acesformat.o /tmp/ccdP8LuY.s 2025-09-09T00:42:26,995 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:27,368 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:27,368 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:27,368 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/acesformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/acesformat.' 2025-09-09T00:42:27,370 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/acrformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/acrformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:27,374 Using built-in specs. 2025-09-09T00:42:27,375 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:27,375 Target: arm-linux-gnueabihf 2025-09-09T00:42:27,375 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:27,375 Thread model: posix 2025-09-09T00:42:27,375 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:27,375 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:27,376 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/acrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:27,376 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/acrformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase acrformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc7MQVEa.s 2025-09-09T00:42:27,386 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:27,386 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:27,386 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:27,386 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:27,386 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:27,386 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:27,387 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:27,387 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:27,387 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:27,387 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:27,387 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:27,387 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:27,387 #include "..." search starts here: 2025-09-09T00:42:27,387 #include <...> search starts here: 2025-09-09T00:42:27,387 /usr/include/eigen3 2025-09-09T00:42:27,388 include 2025-09-09T00:42:27,388 /usr/include/python3.13 2025-09-09T00:42:27,388 /usr/include/c++/14 2025-09-09T00:42:27,388 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:27,388 /usr/include/c++/14/backward 2025-09-09T00:42:27,388 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:27,388 /usr/local/include 2025-09-09T00:42:27,388 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:27,388 /usr/include 2025-09-09T00:42:27,388 End of search list. 2025-09-09T00:42:27,402 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:28,922 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:28,922 from include/openbabel/mol.h:43, 2025-09-09T00:42:28,922 from ./src/formats/acrformat.cpp:23: 2025-09-09T00:42:28,922 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:28,923 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:28,923 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:28,923 | ^ 2025-09-09T00:42:28,923 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:28,923 37 | # define UNUSED(x) x 2025-09-09T00:42:28,923 | ^ 2025-09-09T00:42:29,537 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:29,537 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:29,537 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:29,537 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:29,537 | ^ 2025-09-09T00:42:29,538 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:29,538 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:29,538 | ^~~~~~~~ 2025-09-09T00:42:29,541 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:29,541 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:29,541 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:29,541 | ^ 2025-09-09T00:42:29,542 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:29,542 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:29,542 | ^~~~~~~~ 2025-09-09T00:42:29,556 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:29,556 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:29,556 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:29,556 | ^ 2025-09-09T00:42:29,556 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:29,556 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:29,556 | ^~~~~~~~ 2025-09-09T00:42:29,561 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:29,561 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:29,561 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:29,561 | ^ 2025-09-09T00:42:29,561 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:29,561 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:29,562 | ^~~~~~~~ 2025-09-09T00:42:29,705 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:29,706 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:29,706 from include/openbabel/obmolecformat.h:31, 2025-09-09T00:42:29,706 from ./src/formats/acrformat.cpp:24: 2025-09-09T00:42:29,706 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:29,706 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:29,706 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:29,706 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:29,706 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:29,707 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:29,707 from include/openbabel/mol.h:35: 2025-09-09T00:42:29,707 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:29,707 131 | struct binary_function 2025-09-09T00:42:29,707 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:29,869 ./src/formats/acrformat.cpp: In member function ‘virtual int OpenBabel::ACRFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:42:29,869 ./src/formats/acrformat.cpp:67:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:42:29,869 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:42:29,869 | ~~~~^ 2025-09-09T00:42:29,870 ./src/formats/acrformat.cpp:67:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:42:29,870 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:42:29,870 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:42:29,873 ./src/formats/acrformat.cpp: In member function ‘virtual bool OpenBabel::ACRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:29,873 ./src/formats/acrformat.cpp:113:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:42:29,873 113 | } else if (sscanf(buf, "Number of Atoms in Crystal=%d\n", &tmp)) { 2025-09-09T00:42:29,873 | ~^ ~~~~ 2025-09-09T00:42:29,873 | | | 2025-09-09T00:42:29,873 | int* unsigned int* 2025-09-09T00:42:29,873 | %d 2025-09-09T00:42:29,874 ./src/formats/acrformat.cpp:120:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:42:29,874 120 | } else if (sscanf(buf, "Number of Links in Crystal=%d\n", &tmp)) { 2025-09-09T00:42:29,874 | ~^ ~~~~ 2025-09-09T00:42:29,874 | | | 2025-09-09T00:42:29,874 | int* unsigned int* 2025-09-09T00:42:29,874 | %d 2025-09-09T00:42:31,434 ./src/formats/acrformat.cpp:163:12: warning: ‘atoms’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:42:31,434 163 | } else if ( pmol->NumAtoms() != atoms ) { 2025-09-09T00:42:31,434 | ^~ 2025-09-09T00:42:31,434 ./src/formats/acrformat.cpp:92:18: note: ‘atoms’ was declared here 2025-09-09T00:42:31,434 92 | unsigned int atoms, bonds, tmp; 2025-09-09T00:42:31,434 | ^~~~~ 2025-09-09T00:42:31,434 ./src/formats/acrformat.cpp:159:5: warning: ‘bonds’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:42:31,435 159 | if ( pmol->NumBonds() != bonds ) { 2025-09-09T00:42:31,435 | ^~ 2025-09-09T00:42:31,435 ./src/formats/acrformat.cpp:92:25: note: ‘bonds’ was declared here 2025-09-09T00:42:31,435 92 | unsigned int atoms, bonds, tmp; 2025-09-09T00:42:31,435 | ^~~~~ 2025-09-09T00:42:32,156 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/acrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:32,157 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/acrformat.o /tmp/cc7MQVEa.s 2025-09-09T00:42:32,165 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:32,370 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:32,371 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:32,371 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/acrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/acrformat.' 2025-09-09T00:42:32,372 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/adfformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/adfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:32,376 Using built-in specs. 2025-09-09T00:42:32,377 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:32,377 Target: arm-linux-gnueabihf 2025-09-09T00:42:32,377 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:32,377 Thread model: posix 2025-09-09T00:42:32,377 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:32,377 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:32,378 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/adfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:32,378 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/adfformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase adfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccrGsIKc.s 2025-09-09T00:42:32,389 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:32,389 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:32,389 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:32,389 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:32,389 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:32,390 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:32,390 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:32,390 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:32,390 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:32,390 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:32,390 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:32,390 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:32,390 #include "..." search starts here: 2025-09-09T00:42:32,391 #include <...> search starts here: 2025-09-09T00:42:32,391 /usr/include/eigen3 2025-09-09T00:42:32,391 include 2025-09-09T00:42:32,391 /usr/include/python3.13 2025-09-09T00:42:32,391 /usr/include/c++/14 2025-09-09T00:42:32,391 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:32,391 /usr/include/c++/14/backward 2025-09-09T00:42:32,391 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:32,391 /usr/local/include 2025-09-09T00:42:32,392 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:32,392 /usr/include 2025-09-09T00:42:32,392 End of search list. 2025-09-09T00:42:32,407 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:33,873 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:33,873 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:33,873 from ./src/formats/adfformat.cpp:34: 2025-09-09T00:42:33,874 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:33,874 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:33,874 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:33,874 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:42:33,874 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:42:33,874 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:42:33,874 from /usr/include/c++/14/ios:44, 2025-09-09T00:42:33,874 from /usr/include/c++/14/istream:40, 2025-09-09T00:42:33,874 from /usr/include/c++/14/fstream:40, 2025-09-09T00:42:33,875 from ./src/formats/adfformat.cpp:28: 2025-09-09T00:42:33,875 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:33,875 131 | struct binary_function 2025-09-09T00:42:33,875 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:34,045 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:34,045 from include/openbabel/mol.h:43, 2025-09-09T00:42:34,045 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:34,046 from ./src/formats/adfformat.cpp:35: 2025-09-09T00:42:34,046 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:34,046 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:34,046 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:34,046 | ^ 2025-09-09T00:42:34,046 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:34,046 37 | # define UNUSED(x) x 2025-09-09T00:42:34,046 | ^ 2025-09-09T00:42:34,585 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:34,585 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:34,585 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:34,585 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:34,585 | ^ 2025-09-09T00:42:34,585 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:34,585 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:34,586 | ^~~~~~~~ 2025-09-09T00:42:34,588 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:34,589 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:34,589 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:34,589 | ^ 2025-09-09T00:42:34,589 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:34,589 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:34,589 | ^~~~~~~~ 2025-09-09T00:42:34,603 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:34,603 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:34,603 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:34,603 | ^ 2025-09-09T00:42:34,603 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:34,604 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:34,604 | ^~~~~~~~ 2025-09-09T00:42:34,608 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:34,608 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:34,608 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:34,608 | ^ 2025-09-09T00:42:34,608 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:34,608 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:34,609 | ^~~~~~~~ 2025-09-09T00:42:34,816 include/openbabel/base.h: At global scope: 2025-09-09T00:42:34,816 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:42:34,816 229 | virtual const std::string &GetValue() const 2025-09-09T00:42:34,816 | ^~~~~~~~ 2025-09-09T00:42:34,816 In file included from ./src/formats/adfformat.cpp:37: 2025-09-09T00:42:34,816 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:42:34,816 76 | double GetValue (vector3 pos) const; 2025-09-09T00:42:34,817 | ^~~~~~~~ 2025-09-09T00:42:34,830 ./src/formats/adfformat.cpp: In member function ‘virtual bool OpenBabel::ADFInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:34,830 ./src/formats/adfformat.cpp:274:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2025-09-09T00:42:34,830 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2025-09-09T00:42:34,830 | ~~~~~~~~^~~ 2025-09-09T00:42:34,830 ./src/formats/adfformat.cpp:274:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:42:34,830 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2025-09-09T00:42:34,831 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:42:34,841 ./src/formats/adfformat.cpp: In member function ‘virtual int OpenBabel::OBT41Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:42:34,841 ./src/formats/adfformat.cpp:400:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:42:34,841 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2025-09-09T00:42:34,841 | ~~~~^ 2025-09-09T00:42:34,841 ./src/formats/adfformat.cpp:400:51: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:42:34,841 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2025-09-09T00:42:34,841 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:42:34,844 ./src/formats/adfformat.cpp: In member function ‘void OpenBabel::OBT41Format::AddSCFGrids(std::istream&, OpenBabel::OBGridData&)’: 2025-09-09T00:42:34,844 ./src/formats/adfformat.cpp:448:32: warning: unused parameter ‘is’ [-Wunused-parameter] 2025-09-09T00:42:34,844 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2025-09-09T00:42:34,844 | ~~~~~~~~~^~ 2025-09-09T00:42:34,844 ./src/formats/adfformat.cpp:448:48: warning: unused parameter ‘t41’ [-Wunused-parameter] 2025-09-09T00:42:34,844 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2025-09-09T00:42:34,844 | ~~~~~~~~~~~~^~~ 2025-09-09T00:42:34,847 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadBinary(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:34,847 ./src/formats/adfformat.cpp:533:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2025-09-09T00:42:34,847 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2025-09-09T00:42:34,847 | ~~~~~~~~^~~ 2025-09-09T00:42:34,848 ./src/formats/adfformat.cpp:533:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:42:34,848 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2025-09-09T00:42:34,848 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:42:34,853 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadASCII(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:34,854 ./src/formats/adfformat.cpp:590:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:42:34,854 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,854 | ^~~~~ 2025-09-09T00:42:34,854 ./src/formats/adfformat.cpp:590:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:42:34,854 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,854 | ^~~~ 2025-09-09T00:42:34,858 ./src/formats/adfformat.cpp:603:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:42:34,858 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,858 | ^~~~~ 2025-09-09T00:42:34,858 ./src/formats/adfformat.cpp:603:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:42:34,858 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,859 | ^~~~ 2025-09-09T00:42:34,873 ./src/formats/adfformat.cpp:625:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:42:34,873 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,873 | ^~~~~ 2025-09-09T00:42:34,873 ./src/formats/adfformat.cpp:625:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:42:34,873 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,873 | ^~~~ 2025-09-09T00:42:34,878 ./src/formats/adfformat.cpp:640:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:42:34,879 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,879 | ^~~~~ 2025-09-09T00:42:34,879 ./src/formats/adfformat.cpp:640:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:42:34,879 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,879 | ^~~~ 2025-09-09T00:42:34,882 ./src/formats/adfformat.cpp:655:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:42:34,882 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,882 | ^~~~~ 2025-09-09T00:42:34,882 ./src/formats/adfformat.cpp:655:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:42:34,883 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:42:34,883 | ^~~~ 2025-09-09T00:42:41,898 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/adfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:41,898 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/adfformat.o /tmp/ccrGsIKc.s 2025-09-09T00:42:41,903 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:42,560 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:42,560 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:42,560 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/adfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/adfformat.' 2025-09-09T00:42:42,563 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/alchemyformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/alchemyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:42,567 Using built-in specs. 2025-09-09T00:42:42,568 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:42,568 Target: arm-linux-gnueabihf 2025-09-09T00:42:42,568 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:42,568 Thread model: posix 2025-09-09T00:42:42,568 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:42,568 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:42,568 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/alchemyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:42,569 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/alchemyformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase alchemyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccj0PqIc.s 2025-09-09T00:42:42,579 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:42,579 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:42,580 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:42,580 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:42,580 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:42,580 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:42,581 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:42,581 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:42,581 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:42,581 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:42,581 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:42,581 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:42,582 #include "..." search starts here: 2025-09-09T00:42:42,582 #include <...> search starts here: 2025-09-09T00:42:42,582 /usr/include/eigen3 2025-09-09T00:42:42,582 include 2025-09-09T00:42:42,582 /usr/include/python3.13 2025-09-09T00:42:42,582 /usr/include/c++/14 2025-09-09T00:42:42,582 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:42,582 /usr/include/c++/14/backward 2025-09-09T00:42:42,583 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:42,583 /usr/local/include 2025-09-09T00:42:42,583 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:42,583 /usr/include 2025-09-09T00:42:42,583 End of search list. 2025-09-09T00:42:42,601 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:44,107 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:44,107 from include/openbabel/mol.h:43, 2025-09-09T00:42:44,107 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:44,107 from ./src/formats/alchemyformat.cpp:17: 2025-09-09T00:42:44,108 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:44,108 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:44,108 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:44,108 | ^ 2025-09-09T00:42:44,108 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:44,108 37 | # define UNUSED(x) x 2025-09-09T00:42:44,108 | ^ 2025-09-09T00:42:44,719 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:44,719 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:44,719 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:44,719 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:44,719 | ^ 2025-09-09T00:42:44,720 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:44,720 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:44,720 | ^~~~~~~~ 2025-09-09T00:42:44,723 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:44,723 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:44,723 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:44,723 | ^ 2025-09-09T00:42:44,723 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:44,723 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:44,723 | ^~~~~~~~ 2025-09-09T00:42:44,737 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:44,737 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:44,737 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:44,737 | ^ 2025-09-09T00:42:44,738 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:44,738 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:44,738 | ^~~~~~~~ 2025-09-09T00:42:44,742 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:44,742 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:44,742 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:44,743 | ^ 2025-09-09T00:42:44,743 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:44,743 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:44,743 | ^~~~~~~~ 2025-09-09T00:42:44,881 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:44,881 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:44,881 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:44,881 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:44,881 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:44,881 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:44,882 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:44,882 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:44,882 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:44,882 from include/openbabel/mol.h:35: 2025-09-09T00:42:44,882 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:44,882 131 | struct binary_function 2025-09-09T00:42:44,882 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:47,323 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/alchemyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:47,323 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/alchemyformat.o /tmp/ccj0PqIc.s 2025-09-09T00:42:47,328 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:47,523 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:47,523 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:47,523 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/alchemyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/alchemyformat.' 2025-09-09T00:42:47,525 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/amberformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/amberformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:47,530 Using built-in specs. 2025-09-09T00:42:47,530 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:47,530 Target: arm-linux-gnueabihf 2025-09-09T00:42:47,530 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:47,530 Thread model: posix 2025-09-09T00:42:47,530 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:47,530 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:47,530 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/amberformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:47,531 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/amberformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase amberformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccaoJUE9.s 2025-09-09T00:42:47,542 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:47,542 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:47,542 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:47,542 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:47,542 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:47,542 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:47,543 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:47,543 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:47,543 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:47,543 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:47,543 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:47,543 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:47,543 #include "..." search starts here: 2025-09-09T00:42:47,543 #include <...> search starts here: 2025-09-09T00:42:47,544 /usr/include/eigen3 2025-09-09T00:42:47,544 include 2025-09-09T00:42:47,544 /usr/include/python3.13 2025-09-09T00:42:47,544 /usr/include/c++/14 2025-09-09T00:42:47,544 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:47,544 /usr/include/c++/14/backward 2025-09-09T00:42:47,544 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:47,544 /usr/local/include 2025-09-09T00:42:47,544 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:47,545 /usr/include 2025-09-09T00:42:47,545 End of search list. 2025-09-09T00:42:47,563 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:49,075 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:49,075 from include/openbabel/mol.h:43, 2025-09-09T00:42:49,076 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:49,076 from ./src/formats/amberformat.cpp:17: 2025-09-09T00:42:49,076 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:49,076 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:49,076 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:49,076 | ^ 2025-09-09T00:42:49,076 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:49,076 37 | # define UNUSED(x) x 2025-09-09T00:42:49,076 | ^ 2025-09-09T00:42:49,687 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:49,687 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:49,688 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:49,688 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:49,688 | ^ 2025-09-09T00:42:49,688 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:49,688 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:49,688 | ^~~~~~~~ 2025-09-09T00:42:49,692 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:49,692 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:49,692 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:49,693 | ^ 2025-09-09T00:42:49,693 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:49,693 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:49,693 | ^~~~~~~~ 2025-09-09T00:42:49,707 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:49,708 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:49,708 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:49,708 | ^ 2025-09-09T00:42:49,708 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:49,708 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:49,708 | ^~~~~~~~ 2025-09-09T00:42:49,713 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:49,714 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:49,714 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:49,714 | ^ 2025-09-09T00:42:49,714 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:49,714 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:49,714 | ^~~~~~~~ 2025-09-09T00:42:49,853 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:49,853 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:49,853 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:49,853 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:49,853 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:49,853 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:49,853 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:49,854 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:49,854 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:49,854 from include/openbabel/mol.h:35: 2025-09-09T00:42:49,854 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:49,854 131 | struct binary_function 2025-09-09T00:42:49,855 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:52,094 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/amberformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:52,095 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/amberformat.o /tmp/ccaoJUE9.s 2025-09-09T00:42:52,100 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:52,272 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:52,272 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:52,273 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/amberformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/amberformat.' 2025-09-09T00:42:52,274 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/aoforceformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/aoforceformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:52,279 Using built-in specs. 2025-09-09T00:42:52,280 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:52,280 Target: arm-linux-gnueabihf 2025-09-09T00:42:52,281 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:52,281 Thread model: posix 2025-09-09T00:42:52,281 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:52,281 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:52,282 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/aoforceformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:52,283 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/aoforceformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase aoforceformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccECUk6T.s 2025-09-09T00:42:52,298 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:52,298 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:52,298 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:52,299 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:52,300 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:52,300 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:52,300 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:52,300 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:52,300 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:52,301 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:52,301 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:52,301 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:52,301 #include "..." search starts here: 2025-09-09T00:42:52,301 #include <...> search starts here: 2025-09-09T00:42:52,301 /usr/include/eigen3 2025-09-09T00:42:52,302 include 2025-09-09T00:42:52,302 /usr/include/python3.13 2025-09-09T00:42:52,302 /usr/include/c++/14 2025-09-09T00:42:52,302 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:52,302 /usr/include/c++/14/backward 2025-09-09T00:42:52,303 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:52,303 /usr/local/include 2025-09-09T00:42:52,303 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:52,303 /usr/include 2025-09-09T00:42:52,303 End of search list. 2025-09-09T00:42:52,320 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:53,831 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:53,832 from include/openbabel/mol.h:43, 2025-09-09T00:42:53,832 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:53,832 from ./src/formats/aoforceformat.cpp:17: 2025-09-09T00:42:53,832 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:53,832 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:53,832 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:53,832 | ^ 2025-09-09T00:42:53,832 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:53,832 37 | # define UNUSED(x) x 2025-09-09T00:42:53,832 | ^ 2025-09-09T00:42:54,444 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:54,445 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:54,445 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:54,445 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:54,445 | ^ 2025-09-09T00:42:54,445 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:54,445 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:54,445 | ^~~~~~~~ 2025-09-09T00:42:54,449 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:54,450 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:54,450 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:54,450 | ^ 2025-09-09T00:42:54,450 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:54,450 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:54,450 | ^~~~~~~~ 2025-09-09T00:42:54,465 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:54,465 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:54,465 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:54,465 | ^ 2025-09-09T00:42:54,465 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:54,465 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:54,465 | ^~~~~~~~ 2025-09-09T00:42:54,471 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:54,471 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:54,471 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:54,471 | ^ 2025-09-09T00:42:54,471 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:54,471 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:54,471 | ^~~~~~~~ 2025-09-09T00:42:54,610 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:54,611 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:54,611 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:54,611 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:54,611 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:54,611 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:54,611 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:54,612 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:54,612 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:54,612 from include/openbabel/mol.h:35: 2025-09-09T00:42:54,612 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:54,612 131 | struct binary_function 2025-09-09T00:42:54,612 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:58,523 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/aoforceformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:58,524 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/aoforceformat.o /tmp/ccECUk6T.s 2025-09-09T00:42:58,529 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:58,873 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:42:58,874 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:42:58,874 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/aoforceformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/aoforceformat.' 2025-09-09T00:42:58,876 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/asciiformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/asciiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:42:58,880 Using built-in specs. 2025-09-09T00:42:58,881 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:58,881 Target: arm-linux-gnueabihf 2025-09-09T00:42:58,881 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:42:58,881 Thread model: posix 2025-09-09T00:42:58,882 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:58,882 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:58,882 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/asciiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:42:58,882 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/asciiformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase asciiformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccVah06b.s 2025-09-09T00:42:58,894 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:58,894 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:42:58,894 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:58,894 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:58,894 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:58,895 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:58,895 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:58,895 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:58,895 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:58,895 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:58,895 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:58,895 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:58,896 #include "..." search starts here: 2025-09-09T00:42:58,896 #include <...> search starts here: 2025-09-09T00:42:58,896 /usr/include/eigen3 2025-09-09T00:42:58,896 include 2025-09-09T00:42:58,896 /usr/include/python3.13 2025-09-09T00:42:58,896 /usr/include/c++/14 2025-09-09T00:42:58,896 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:58,896 /usr/include/c++/14/backward 2025-09-09T00:42:58,897 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:58,897 /usr/local/include 2025-09-09T00:42:58,897 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:58,897 /usr/include 2025-09-09T00:42:58,897 End of search list. 2025-09-09T00:42:58,913 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:00,415 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:00,415 from include/openbabel/mol.h:43, 2025-09-09T00:43:00,415 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:00,415 from ./src/formats/asciiformat.cpp:19: 2025-09-09T00:43:00,416 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:00,416 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:00,416 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:00,416 | ^ 2025-09-09T00:43:00,416 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:00,416 37 | # define UNUSED(x) x 2025-09-09T00:43:00,416 | ^ 2025-09-09T00:43:01,027 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:01,028 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:01,028 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:01,028 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:01,028 | ^ 2025-09-09T00:43:01,028 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:01,028 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:01,028 | ^~~~~~~~ 2025-09-09T00:43:01,031 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:01,032 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:01,032 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:01,032 | ^ 2025-09-09T00:43:01,032 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:01,032 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:01,032 | ^~~~~~~~ 2025-09-09T00:43:01,046 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:01,046 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:01,046 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:01,046 | ^ 2025-09-09T00:43:01,046 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:01,046 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:01,046 | ^~~~~~~~ 2025-09-09T00:43:01,051 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:01,051 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:01,051 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:01,051 | ^ 2025-09-09T00:43:01,051 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:01,051 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:01,052 | ^~~~~~~~ 2025-09-09T00:43:01,190 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:01,190 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:01,190 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:01,190 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:01,190 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:01,190 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:01,190 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:01,190 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:01,191 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:01,191 from include/openbabel/mol.h:35: 2025-09-09T00:43:01,191 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:01,191 131 | struct binary_function 2025-09-09T00:43:01,191 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:01,390 In file included from ./src/formats/asciiformat.cpp:22: 2025-09-09T00:43:01,390 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:43:01,390 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:43:01,390 34 | void SetFontFamily(const std::string &fontFamily) {} 2025-09-09T00:43:01,390 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:43:03,531 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/asciiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:03,531 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/asciiformat.o /tmp/ccVah06b.s 2025-09-09T00:43:03,540 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:03,747 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:03,748 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:03,748 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/asciiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/asciiformat.' 2025-09-09T00:43:03,748 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/balstformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/balstformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:03,753 Using built-in specs. 2025-09-09T00:43:03,753 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:03,754 Target: arm-linux-gnueabihf 2025-09-09T00:43:03,754 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:03,754 Thread model: posix 2025-09-09T00:43:03,754 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:03,754 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:03,754 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/balstformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:03,754 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/balstformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase balstformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccRFaxoI.s 2025-09-09T00:43:03,764 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:03,764 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:03,764 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:03,765 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:03,765 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:03,765 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:03,770 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:03,770 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:03,770 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:03,770 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:03,770 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:03,771 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:03,771 #include "..." search starts here: 2025-09-09T00:43:03,771 #include <...> search starts here: 2025-09-09T00:43:03,771 /usr/include/eigen3 2025-09-09T00:43:03,771 include 2025-09-09T00:43:03,771 /usr/include/python3.13 2025-09-09T00:43:03,771 /usr/include/c++/14 2025-09-09T00:43:03,772 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:03,772 /usr/include/c++/14/backward 2025-09-09T00:43:03,772 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:03,772 /usr/local/include 2025-09-09T00:43:03,772 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:03,772 /usr/include 2025-09-09T00:43:03,772 End of search list. 2025-09-09T00:43:03,790 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:05,298 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:05,298 from include/openbabel/mol.h:43, 2025-09-09T00:43:05,298 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:05,298 from ./src/formats/balstformat.cpp:17: 2025-09-09T00:43:05,298 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:05,299 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:05,299 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:05,299 | ^ 2025-09-09T00:43:05,299 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:05,299 37 | # define UNUSED(x) x 2025-09-09T00:43:05,299 | ^ 2025-09-09T00:43:05,908 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:05,908 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:05,908 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:05,908 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:05,908 | ^ 2025-09-09T00:43:05,908 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:05,908 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:05,908 | ^~~~~~~~ 2025-09-09T00:43:05,912 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:05,913 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:05,913 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:05,913 | ^ 2025-09-09T00:43:05,913 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:05,913 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:05,913 | ^~~~~~~~ 2025-09-09T00:43:05,928 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:05,928 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:05,928 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:05,928 | ^ 2025-09-09T00:43:05,928 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:05,929 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:05,929 | ^~~~~~~~ 2025-09-09T00:43:05,934 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:05,934 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:05,934 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:05,934 | ^ 2025-09-09T00:43:05,934 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:05,935 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:05,935 | ^~~~~~~~ 2025-09-09T00:43:06,074 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:06,074 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:06,074 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:06,074 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:06,074 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:06,074 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:06,075 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:06,075 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:06,076 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:06,076 from include/openbabel/mol.h:35: 2025-09-09T00:43:06,076 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:06,076 131 | struct binary_function 2025-09-09T00:43:06,076 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:08,392 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/balstformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:08,392 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/balstformat.o /tmp/ccRFaxoI.s 2025-09-09T00:43:08,397 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:08,578 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:08,578 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:08,578 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/balstformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/balstformat.' 2025-09-09T00:43:08,578 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/bgfformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/bgfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:08,582 Using built-in specs. 2025-09-09T00:43:08,583 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:08,583 Target: arm-linux-gnueabihf 2025-09-09T00:43:08,583 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:08,584 Thread model: posix 2025-09-09T00:43:08,584 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:08,584 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:08,584 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/bgfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:08,584 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/bgfformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase bgfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc5xB3aR.s 2025-09-09T00:43:08,594 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:08,594 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:08,595 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:08,595 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:08,595 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:08,595 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:08,595 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:08,595 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:08,595 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:08,595 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:08,595 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:08,596 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:08,596 #include "..." search starts here: 2025-09-09T00:43:08,596 #include <...> search starts here: 2025-09-09T00:43:08,596 /usr/include/eigen3 2025-09-09T00:43:08,596 include 2025-09-09T00:43:08,596 /usr/include/python3.13 2025-09-09T00:43:08,596 /usr/include/c++/14 2025-09-09T00:43:08,596 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:08,596 /usr/include/c++/14/backward 2025-09-09T00:43:08,596 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:08,597 /usr/local/include 2025-09-09T00:43:08,597 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:08,597 /usr/include 2025-09-09T00:43:08,597 End of search list. 2025-09-09T00:43:08,611 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:10,123 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:10,124 from include/openbabel/mol.h:43, 2025-09-09T00:43:10,124 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:10,124 from ./src/formats/bgfformat.cpp:17: 2025-09-09T00:43:10,124 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:10,124 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:10,124 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:10,124 | ^ 2025-09-09T00:43:10,124 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:10,124 37 | # define UNUSED(x) x 2025-09-09T00:43:10,125 | ^ 2025-09-09T00:43:10,735 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:10,736 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:10,736 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:10,736 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:10,736 | ^ 2025-09-09T00:43:10,736 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:10,736 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:10,736 | ^~~~~~~~ 2025-09-09T00:43:10,739 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:10,739 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:10,739 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:10,740 | ^ 2025-09-09T00:43:10,740 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:10,740 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:10,740 | ^~~~~~~~ 2025-09-09T00:43:10,754 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:10,754 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:10,754 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:10,754 | ^ 2025-09-09T00:43:10,754 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:10,754 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:10,754 | ^~~~~~~~ 2025-09-09T00:43:10,759 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:10,759 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:10,759 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:10,759 | ^ 2025-09-09T00:43:10,759 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:10,759 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:10,759 | ^~~~~~~~ 2025-09-09T00:43:10,898 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:10,898 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:10,898 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:10,898 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:10,898 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:10,898 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:10,898 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:10,898 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:10,898 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:10,899 from include/openbabel/mol.h:35: 2025-09-09T00:43:10,899 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:10,899 131 | struct binary_function 2025-09-09T00:43:10,899 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:14,027 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/bgfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:14,028 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/bgfformat.o /tmp/cc5xB3aR.s 2025-09-09T00:43:14,033 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:14,299 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:14,300 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:14,300 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/bgfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/bgfformat.' 2025-09-09T00:43:14,301 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/boxformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/boxformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:14,305 Using built-in specs. 2025-09-09T00:43:14,306 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:14,306 Target: arm-linux-gnueabihf 2025-09-09T00:43:14,306 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:14,306 Thread model: posix 2025-09-09T00:43:14,306 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:14,306 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:14,307 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/boxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:14,307 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/boxformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase boxformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccOt1pI5.s 2025-09-09T00:43:14,317 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:14,318 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:14,318 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:14,318 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:14,318 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:14,318 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:14,318 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:14,319 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:14,319 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:14,319 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:14,319 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:14,319 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:14,319 #include "..." search starts here: 2025-09-09T00:43:14,319 #include <...> search starts here: 2025-09-09T00:43:14,319 /usr/include/eigen3 2025-09-09T00:43:14,320 include 2025-09-09T00:43:14,320 /usr/include/python3.13 2025-09-09T00:43:14,320 /usr/include/c++/14 2025-09-09T00:43:14,320 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:14,320 /usr/include/c++/14/backward 2025-09-09T00:43:14,320 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:14,320 /usr/local/include 2025-09-09T00:43:14,320 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:14,321 /usr/include 2025-09-09T00:43:14,321 End of search list. 2025-09-09T00:43:14,337 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:15,847 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:15,847 from include/openbabel/mol.h:43, 2025-09-09T00:43:15,847 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:15,847 from ./src/formats/boxformat.cpp:17: 2025-09-09T00:43:15,847 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:15,847 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:15,847 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:15,847 | ^ 2025-09-09T00:43:15,847 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:15,848 37 | # define UNUSED(x) x 2025-09-09T00:43:15,848 | ^ 2025-09-09T00:43:16,459 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:16,459 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:16,459 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:16,459 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:16,459 | ^ 2025-09-09T00:43:16,459 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:16,460 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:16,460 | ^~~~~~~~ 2025-09-09T00:43:16,463 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:16,463 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:16,463 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:16,463 | ^ 2025-09-09T00:43:16,463 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:16,463 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:16,464 | ^~~~~~~~ 2025-09-09T00:43:16,477 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:16,477 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:16,477 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:16,478 | ^ 2025-09-09T00:43:16,478 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:16,478 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:16,478 | ^~~~~~~~ 2025-09-09T00:43:16,482 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:16,482 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:16,482 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:16,483 | ^ 2025-09-09T00:43:16,483 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:16,483 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:16,483 | ^~~~~~~~ 2025-09-09T00:43:16,621 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:16,621 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:16,621 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:16,621 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:16,621 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:16,622 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:16,622 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:16,622 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:16,622 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:16,622 from include/openbabel/mol.h:35: 2025-09-09T00:43:16,622 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:16,622 131 | struct binary_function 2025-09-09T00:43:16,622 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:19,190 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/boxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:19,190 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/boxformat.o /tmp/ccOt1pI5.s 2025-09-09T00:43:19,195 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:19,411 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:19,411 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:19,412 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/boxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/boxformat.' 2025-09-09T00:43:19,413 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/cacaoformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/cacaoformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:19,417 Using built-in specs. 2025-09-09T00:43:19,418 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:19,418 Target: arm-linux-gnueabihf 2025-09-09T00:43:19,418 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:19,418 Thread model: posix 2025-09-09T00:43:19,418 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:19,418 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:19,418 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cacaoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:19,418 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cacaoformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase cacaoformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccyIBVrP.s 2025-09-09T00:43:19,428 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:19,428 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:19,428 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:19,428 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:19,429 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:19,429 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:19,429 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:19,429 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:19,429 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:19,429 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:19,429 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:19,429 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:19,429 #include "..." search starts here: 2025-09-09T00:43:19,430 #include <...> search starts here: 2025-09-09T00:43:19,430 /usr/include/eigen3 2025-09-09T00:43:19,430 include 2025-09-09T00:43:19,430 /usr/include/python3.13 2025-09-09T00:43:19,430 /usr/include/c++/14 2025-09-09T00:43:19,430 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:19,430 /usr/include/c++/14/backward 2025-09-09T00:43:19,430 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:19,430 /usr/local/include 2025-09-09T00:43:19,430 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:19,430 /usr/include 2025-09-09T00:43:19,430 End of search list. 2025-09-09T00:43:19,447 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:20,955 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:20,955 from include/openbabel/mol.h:43, 2025-09-09T00:43:20,955 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:20,956 from ./src/formats/cacaoformat.cpp:17: 2025-09-09T00:43:20,956 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:20,956 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:20,956 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:20,956 | ^ 2025-09-09T00:43:20,956 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:20,956 37 | # define UNUSED(x) x 2025-09-09T00:43:20,956 | ^ 2025-09-09T00:43:21,567 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:21,567 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:21,567 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:21,567 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:21,568 | ^ 2025-09-09T00:43:21,568 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:21,568 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:21,568 | ^~~~~~~~ 2025-09-09T00:43:21,571 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:21,571 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:21,571 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:21,571 | ^ 2025-09-09T00:43:21,571 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:21,571 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:21,572 | ^~~~~~~~ 2025-09-09T00:43:21,585 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:21,585 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:21,586 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:21,586 | ^ 2025-09-09T00:43:21,586 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:21,586 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:21,586 | ^~~~~~~~ 2025-09-09T00:43:21,590 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:21,591 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:21,591 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:21,591 | ^ 2025-09-09T00:43:21,591 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:21,591 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:21,591 | ^~~~~~~~ 2025-09-09T00:43:21,729 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:21,729 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:21,729 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:21,729 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:21,730 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:21,730 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:21,730 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:21,730 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:21,730 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:21,730 from include/openbabel/mol.h:35: 2025-09-09T00:43:21,730 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:21,730 131 | struct binary_function 2025-09-09T00:43:21,730 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:24,562 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cacaoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:24,562 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/cacaoformat.o /tmp/ccyIBVrP.s 2025-09-09T00:43:24,570 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:24,804 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:24,804 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:24,804 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cacaoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/cacaoformat.' 2025-09-09T00:43:24,805 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/cacheformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/cacheformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:24,810 Using built-in specs. 2025-09-09T00:43:24,810 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:24,810 Target: arm-linux-gnueabihf 2025-09-09T00:43:24,810 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:24,810 Thread model: posix 2025-09-09T00:43:24,810 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:24,811 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:24,811 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cacheformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:24,811 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cacheformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase cacheformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccqH5GK3.s 2025-09-09T00:43:24,820 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:24,820 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:24,821 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:24,821 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:24,821 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:24,821 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:24,821 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:24,822 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:24,822 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:24,822 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:24,822 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:24,822 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:24,822 #include "..." search starts here: 2025-09-09T00:43:24,823 #include <...> search starts here: 2025-09-09T00:43:24,823 /usr/include/eigen3 2025-09-09T00:43:24,823 include 2025-09-09T00:43:24,823 /usr/include/python3.13 2025-09-09T00:43:24,823 /usr/include/c++/14 2025-09-09T00:43:24,823 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:24,824 /usr/include/c++/14/backward 2025-09-09T00:43:24,824 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:24,824 /usr/local/include 2025-09-09T00:43:24,824 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:24,824 /usr/include 2025-09-09T00:43:24,824 End of search list. 2025-09-09T00:43:24,843 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:26,366 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:26,366 from include/openbabel/mol.h:43, 2025-09-09T00:43:26,366 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:26,366 from ./src/formats/cacheformat.cpp:16: 2025-09-09T00:43:26,366 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:26,366 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:26,366 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:26,366 | ^ 2025-09-09T00:43:26,366 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:26,367 37 | # define UNUSED(x) x 2025-09-09T00:43:26,367 | ^ 2025-09-09T00:43:26,977 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:26,977 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:26,977 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:26,977 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:26,978 | ^ 2025-09-09T00:43:26,978 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:26,978 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:26,978 | ^~~~~~~~ 2025-09-09T00:43:26,982 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:26,982 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:26,982 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:26,982 | ^ 2025-09-09T00:43:26,983 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:26,983 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:26,983 | ^~~~~~~~ 2025-09-09T00:43:26,997 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:26,997 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:26,998 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:26,998 | ^ 2025-09-09T00:43:26,998 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:26,998 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:26,998 | ^~~~~~~~ 2025-09-09T00:43:27,003 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:27,003 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:27,004 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:27,004 | ^ 2025-09-09T00:43:27,004 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:27,004 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:27,004 | ^~~~~~~~ 2025-09-09T00:43:27,143 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:27,143 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:27,143 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:27,143 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:27,143 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:27,143 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:27,144 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:27,144 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:27,145 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:27,145 from include/openbabel/mol.h:35: 2025-09-09T00:43:27,145 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:27,145 131 | struct binary_function 2025-09-09T00:43:27,145 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:29,213 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cacheformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:29,213 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/cacheformat.o /tmp/ccqH5GK3.s 2025-09-09T00:43:29,218 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:29,384 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:29,384 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:29,384 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cacheformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/cacheformat.' 2025-09-09T00:43:29,386 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/carformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/carformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:29,390 Using built-in specs. 2025-09-09T00:43:29,391 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:29,391 Target: arm-linux-gnueabihf 2025-09-09T00:43:29,392 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:29,392 Thread model: posix 2025-09-09T00:43:29,392 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:29,392 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:29,393 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/carformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:29,395 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/carformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase carformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccH7wQ7p.s 2025-09-09T00:43:29,406 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:29,406 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:29,407 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:29,407 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:29,408 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:29,408 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:29,408 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:29,408 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:29,408 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:29,409 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:29,409 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:29,409 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:29,409 #include "..." search starts here: 2025-09-09T00:43:29,409 #include <...> search starts here: 2025-09-09T00:43:29,409 /usr/include/eigen3 2025-09-09T00:43:29,409 include 2025-09-09T00:43:29,410 /usr/include/python3.13 2025-09-09T00:43:29,410 /usr/include/c++/14 2025-09-09T00:43:29,410 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:29,410 /usr/include/c++/14/backward 2025-09-09T00:43:29,410 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:29,410 /usr/local/include 2025-09-09T00:43:29,411 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:29,411 /usr/include 2025-09-09T00:43:29,411 End of search list. 2025-09-09T00:43:29,429 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:30,949 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:30,950 from include/openbabel/mol.h:43, 2025-09-09T00:43:30,950 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:30,950 from ./src/formats/carformat.cpp:18: 2025-09-09T00:43:30,950 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:30,950 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:30,950 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:30,950 | ^ 2025-09-09T00:43:30,950 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:30,950 37 | # define UNUSED(x) x 2025-09-09T00:43:30,950 | ^ 2025-09-09T00:43:31,562 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:31,562 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,563 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,563 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:31,563 | ^ 2025-09-09T00:43:31,563 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:31,563 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:31,563 | ^~~~~~~~ 2025-09-09T00:43:31,567 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,567 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,567 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:31,568 | ^ 2025-09-09T00:43:31,568 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:31,568 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:31,568 | ^~~~~~~~ 2025-09-09T00:43:31,582 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,583 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,583 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:31,583 | ^ 2025-09-09T00:43:31,583 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:31,583 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:31,583 | ^~~~~~~~ 2025-09-09T00:43:31,588 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,589 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,589 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:31,589 | ^ 2025-09-09T00:43:31,589 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:31,589 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:31,589 | ^~~~~~~~ 2025-09-09T00:43:31,727 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:31,728 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:31,728 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:31,728 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:31,728 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:31,728 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:31,728 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:31,729 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:31,729 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:31,729 from include/openbabel/mol.h:35: 2025-09-09T00:43:31,729 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:31,729 131 | struct binary_function 2025-09-09T00:43:31,730 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:34,195 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/carformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:34,196 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/carformat.o /tmp/ccH7wQ7p.s 2025-09-09T00:43:34,203 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:34,415 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:34,415 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:34,415 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/carformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/carformat.' 2025-09-09T00:43:34,417 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/castepformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/castepformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:34,421 Using built-in specs. 2025-09-09T00:43:34,422 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:34,422 Target: arm-linux-gnueabihf 2025-09-09T00:43:34,422 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:34,422 Thread model: posix 2025-09-09T00:43:34,422 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:34,422 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:34,423 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/castepformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:34,423 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/castepformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase castepformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccyQCcSD.s 2025-09-09T00:43:34,432 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:34,432 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:34,433 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:34,433 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:34,433 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:34,433 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:34,433 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:34,434 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:34,434 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:34,434 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:34,434 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:34,434 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:34,434 #include "..." search starts here: 2025-09-09T00:43:34,434 #include <...> search starts here: 2025-09-09T00:43:34,435 /usr/include/eigen3 2025-09-09T00:43:34,435 include 2025-09-09T00:43:34,435 /usr/include/python3.13 2025-09-09T00:43:34,435 /usr/include/c++/14 2025-09-09T00:43:34,435 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:34,435 /usr/include/c++/14/backward 2025-09-09T00:43:34,435 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:34,435 /usr/local/include 2025-09-09T00:43:34,435 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:34,436 /usr/include 2025-09-09T00:43:34,436 End of search list. 2025-09-09T00:43:34,452 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:35,946 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:35,946 from include/openbabel/mol.h:43, 2025-09-09T00:43:35,946 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:35,947 from ./src/formats/castepformat.cpp:16: 2025-09-09T00:43:35,947 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:35,947 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:35,947 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:35,947 | ^ 2025-09-09T00:43:35,947 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:35,947 37 | # define UNUSED(x) x 2025-09-09T00:43:35,947 | ^ 2025-09-09T00:43:36,559 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:36,559 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,559 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,559 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:36,559 | ^ 2025-09-09T00:43:36,559 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:36,559 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:36,560 | ^~~~~~~~ 2025-09-09T00:43:36,562 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,563 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,563 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:36,563 | ^ 2025-09-09T00:43:36,563 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:36,563 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:36,563 | ^~~~~~~~ 2025-09-09T00:43:36,577 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,577 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,577 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:36,577 | ^ 2025-09-09T00:43:36,577 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:36,578 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:36,578 | ^~~~~~~~ 2025-09-09T00:43:36,582 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,582 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,582 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:36,582 | ^ 2025-09-09T00:43:36,583 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:36,583 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:36,583 | ^~~~~~~~ 2025-09-09T00:43:36,721 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:36,722 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:36,722 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:36,722 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:36,722 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:36,722 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:36,722 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:36,722 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:36,722 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:36,722 from include/openbabel/mol.h:35: 2025-09-09T00:43:36,723 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:36,723 131 | struct binary_function 2025-09-09T00:43:36,723 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:36,890 ./src/formats/castepformat.cpp: In member function ‘virtual int OpenBabel::CASTEPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:43:36,890 ./src/formats/castepformat.cpp:50:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:43:36,890 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:43:36,890 | ~~~~^ 2025-09-09T00:43:36,890 ./src/formats/castepformat.cpp:50:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:43:36,890 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:43:36,890 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:43:38,970 ./src/formats/castepformat.cpp: In member function ‘virtual bool OpenBabel::CASTEPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:38,970 ./src/formats/castepformat.cpp:203:17: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:43:38,970 203 | snprintf(tag, BUFF_SIZE, "%f", enthalpy); 2025-09-09T00:43:38,970 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:38,970 ./src/formats/castepformat.cpp:86:30: note: ‘enthalpy’ was declared here 2025-09-09T00:43:38,970 86 | double pressure, volume, enthalpy; 2025-09-09T00:43:38,971 | ^~~~~~~~ 2025-09-09T00:43:39,544 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/castepformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:39,545 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/castepformat.o /tmp/ccyQCcSD.s 2025-09-09T00:43:39,550 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:39,796 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:39,796 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:39,796 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/castepformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/castepformat.' 2025-09-09T00:43:39,796 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/cccformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/cccformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:39,802 Using built-in specs. 2025-09-09T00:43:39,802 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:39,802 Target: arm-linux-gnueabihf 2025-09-09T00:43:39,802 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:39,802 Thread model: posix 2025-09-09T00:43:39,802 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:39,802 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:39,803 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cccformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:39,803 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cccformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase cccformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccuSupkW.s 2025-09-09T00:43:39,819 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:39,819 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:39,820 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:39,820 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:39,820 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:39,820 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:39,820 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:39,821 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:39,821 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:39,821 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:39,821 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:39,821 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:39,821 #include "..." search starts here: 2025-09-09T00:43:39,821 #include <...> search starts here: 2025-09-09T00:43:39,822 /usr/include/eigen3 2025-09-09T00:43:39,822 include 2025-09-09T00:43:39,822 /usr/include/python3.13 2025-09-09T00:43:39,822 /usr/include/c++/14 2025-09-09T00:43:39,822 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:39,822 /usr/include/c++/14/backward 2025-09-09T00:43:39,822 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:39,823 /usr/local/include 2025-09-09T00:43:39,823 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:39,823 /usr/include 2025-09-09T00:43:39,823 End of search list. 2025-09-09T00:43:39,836 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:41,345 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:41,345 from include/openbabel/mol.h:43, 2025-09-09T00:43:41,345 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:41,346 from ./src/formats/cccformat.cpp:17: 2025-09-09T00:43:41,346 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:41,346 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:41,346 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:41,346 | ^ 2025-09-09T00:43:41,346 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:41,346 37 | # define UNUSED(x) x 2025-09-09T00:43:41,346 | ^ 2025-09-09T00:43:41,960 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:41,960 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:41,960 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:41,961 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:41,961 | ^ 2025-09-09T00:43:41,961 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:41,961 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:41,961 | ^~~~~~~~ 2025-09-09T00:43:41,964 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:41,964 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:41,964 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:41,964 | ^ 2025-09-09T00:43:41,964 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:41,965 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:41,965 | ^~~~~~~~ 2025-09-09T00:43:41,978 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:41,978 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:41,979 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:41,979 | ^ 2025-09-09T00:43:41,979 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:41,979 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:41,979 | ^~~~~~~~ 2025-09-09T00:43:41,983 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:41,984 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:41,984 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:41,984 | ^ 2025-09-09T00:43:41,984 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:41,984 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:41,984 | ^~~~~~~~ 2025-09-09T00:43:42,122 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:42,122 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:42,122 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:42,122 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:42,122 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:42,123 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:42,123 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:42,123 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:42,123 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:42,123 from include/openbabel/mol.h:35: 2025-09-09T00:43:42,123 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:42,123 131 | struct binary_function 2025-09-09T00:43:42,123 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:44,276 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cccformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:44,276 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/cccformat.o /tmp/ccuSupkW.s 2025-09-09T00:43:44,281 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:44,446 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:44,446 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:44,446 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cccformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/cccformat.' 2025-09-09T00:43:44,447 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/chem3dformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/chem3dformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:44,451 Using built-in specs. 2025-09-09T00:43:44,452 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:44,452 Target: arm-linux-gnueabihf 2025-09-09T00:43:44,452 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:44,452 Thread model: posix 2025-09-09T00:43:44,452 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:44,452 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:44,453 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chem3dformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:44,453 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chem3dformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase chem3dformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccv7BVmG.s 2025-09-09T00:43:44,464 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:44,464 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:44,464 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:44,465 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:44,465 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:44,465 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:44,465 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:44,465 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:44,465 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:44,466 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:44,466 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:44,466 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:44,466 #include "..." search starts here: 2025-09-09T00:43:44,466 #include <...> search starts here: 2025-09-09T00:43:44,466 /usr/include/eigen3 2025-09-09T00:43:44,466 include 2025-09-09T00:43:44,466 /usr/include/python3.13 2025-09-09T00:43:44,467 /usr/include/c++/14 2025-09-09T00:43:44,467 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:44,467 /usr/include/c++/14/backward 2025-09-09T00:43:44,467 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:44,467 /usr/local/include 2025-09-09T00:43:44,467 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:44,467 /usr/include 2025-09-09T00:43:44,467 End of search list. 2025-09-09T00:43:44,483 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:46,063 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:46,063 from include/openbabel/mol.h:43, 2025-09-09T00:43:46,063 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:46,063 from ./src/formats/chem3dformat.cpp:18: 2025-09-09T00:43:46,063 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:46,063 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:46,064 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:46,064 | ^ 2025-09-09T00:43:46,064 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:46,064 37 | # define UNUSED(x) x 2025-09-09T00:43:46,064 | ^ 2025-09-09T00:43:46,597 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:46,597 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:46,598 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:46,598 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:46,598 | ^ 2025-09-09T00:43:46,598 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:46,598 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:46,598 | ^~~~~~~~ 2025-09-09T00:43:46,601 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:46,601 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:46,601 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:46,601 | ^ 2025-09-09T00:43:46,602 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:46,602 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:46,602 | ^~~~~~~~ 2025-09-09T00:43:46,615 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:46,616 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:46,616 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:46,616 | ^ 2025-09-09T00:43:46,616 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:46,616 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:46,616 | ^~~~~~~~ 2025-09-09T00:43:46,621 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:46,621 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:46,621 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:46,621 | ^ 2025-09-09T00:43:46,621 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:46,621 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:46,621 | ^~~~~~~~ 2025-09-09T00:43:46,759 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:46,759 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:46,759 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:46,759 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:46,760 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:46,760 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:46,760 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:46,760 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:43:46,760 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:43:46,760 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:43:46,760 from /usr/include/c++/14/ios:44, 2025-09-09T00:43:46,760 from /usr/include/c++/14/ostream:40, 2025-09-09T00:43:46,760 from include/openbabel/math/matrix3x3.h:24, 2025-09-09T00:43:46,761 from ./src/formats/chem3dformat.cpp:17: 2025-09-09T00:43:46,761 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:46,761 131 | struct binary_function 2025-09-09T00:43:46,761 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:48,734 ./src/formats/chem3dformat.cpp: In static member function ‘static bool OpenBabel::CHEM3D1Format::WriteChem3d(std::ostream&, OpenBabel::OBMol&, const char*)’: 2025-09-09T00:43:48,734 ./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=] 2025-09-09T00:43:48,734 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2025-09-09T00:43:48,734 | ^~ 2025-09-09T00:43:48,734 ./src/formats/chem3dformat.cpp:298:51: note: directive argument in the range [-536870912, 536873461] 2025-09-09T00:43:48,735 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2025-09-09T00:43:48,735 | ^~~~ 2025-09-09T00:43:48,735 ./src/formats/chem3dformat.cpp:298:21: note: ‘snprintf’ output between 2 and 11 bytes into a destination of size 4 2025-09-09T00:43:48,735 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2025-09-09T00:43:48,735 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:49,261 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chem3dformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:49,261 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/chem3dformat.o /tmp/ccv7BVmG.s 2025-09-09T00:43:49,266 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:49,471 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:43:49,471 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:43:49,471 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chem3dformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/chem3dformat.' 2025-09-09T00:43:49,473 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/chemdrawcdx.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/chemdrawcdx.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:49,476 Using built-in specs. 2025-09-09T00:43:49,477 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:49,477 Target: arm-linux-gnueabihf 2025-09-09T00:43:49,477 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:43:49,477 Thread model: posix 2025-09-09T00:43:49,478 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:49,478 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:49,478 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawcdx.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:43:49,478 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemdrawcdx.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase chemdrawcdx.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccevQthf.s 2025-09-09T00:43:49,487 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:49,488 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:43:49,488 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:49,488 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:49,488 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:49,488 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:49,488 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:49,488 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:49,489 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:49,489 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:49,489 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:49,489 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:49,489 #include "..." search starts here: 2025-09-09T00:43:49,489 #include <...> search starts here: 2025-09-09T00:43:49,489 /usr/include/eigen3 2025-09-09T00:43:49,489 include 2025-09-09T00:43:49,489 /usr/include/python3.13 2025-09-09T00:43:49,489 /usr/include/c++/14 2025-09-09T00:43:49,490 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:49,490 /usr/include/c++/14/backward 2025-09-09T00:43:49,490 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:49,490 /usr/local/include 2025-09-09T00:43:49,490 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:49,490 /usr/include 2025-09-09T00:43:49,490 End of search list. 2025-09-09T00:43:49,506 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:51,041 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:51,041 from include/openbabel/mol.h:43, 2025-09-09T00:43:51,042 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:51,042 from ./src/formats/chemdrawcdx.cpp:17: 2025-09-09T00:43:51,042 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:51,042 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:51,042 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:51,042 | ^ 2025-09-09T00:43:51,042 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:51,042 37 | # define UNUSED(x) x 2025-09-09T00:43:51,042 | ^ 2025-09-09T00:43:51,654 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:51,654 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:51,655 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:51,655 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:51,655 | ^ 2025-09-09T00:43:51,655 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:51,655 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:51,655 | ^~~~~~~~ 2025-09-09T00:43:51,658 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:51,658 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:51,658 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:51,659 | ^ 2025-09-09T00:43:51,659 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:51,659 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:51,659 | ^~~~~~~~ 2025-09-09T00:43:51,673 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:51,673 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:51,673 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:51,673 | ^ 2025-09-09T00:43:51,673 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:51,673 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:51,674 | ^~~~~~~~ 2025-09-09T00:43:51,678 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:51,678 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:51,678 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:51,678 | ^ 2025-09-09T00:43:51,678 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:51,678 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:51,678 | ^~~~~~~~ 2025-09-09T00:43:51,816 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:51,817 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:51,817 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:51,817 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:51,817 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:51,817 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:51,817 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:51,817 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:51,818 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:51,818 from include/openbabel/mol.h:35: 2025-09-09T00:43:51,818 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:51,818 131 | struct binary_function 2025-09-09T00:43:51,818 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:52,260 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:43:52,260 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:43:52,260 | ^~~~~~~~ 2025-09-09T00:43:52,260 In file included from ./src/formats/chemdrawcdx.cpp:19: 2025-09-09T00:43:52,260 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:43:52,260 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:43:52,260 | ^~~~~~~~ 2025-09-09T00:43:52,260 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:43:52,261 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:52,261 | ^~~~~~~~ 2025-09-09T00:43:52,261 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:43:52,261 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:43:52,261 | ^~~~~~~~ 2025-09-09T00:43:52,370 ./src/formats/chemdrawcdx.cpp: In member function ‘virtual bool OpenBabel::ChemDrawBinaryXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:52,370 ./src/formats/chemdrawcdx.cpp:205:50: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2025-09-09T00:43:52,370 205 | bool ChemDrawBinaryXFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) 2025-09-09T00:43:52,370 | ~~~~~~~~^~~ 2025-09-09T00:43:52,410 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoReaction(OpenBabel::CDXReader&, OpenBabel::OBReaction*)’: 2025-09-09T00:43:52,410 ./src/formats/chemdrawcdx.cpp:331:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:43:52,410 331 | for(unsigned i=0;iNumAtoms();++idx) 2025-09-09T00:43:52,471 | ~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:52,476 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2025-09-09T00:43:52,476 ./src/formats/chemdrawcdx.cpp:454:27: warning: variable ‘hasElement’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:43:52,476 454 | bool isAlias=false, hasElement=false; 2025-09-09T00:43:52,476 | ^~~~~~~~~~ 2025-09-09T00:43:52,481 ./src/formats/chemdrawcdx.cpp:446:84: warning: unused parameter ‘updown’ [-Wunused-parameter] 2025-09-09T00:43:52,481 446 | map& atommap, map& updown) 2025-09-09T00:43:52,482 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2025-09-09T00:43:54,064 ./src/formats/chemdrawcdx.cpp: In member function ‘std::string OpenBabel::ChemDrawBinaryXFormat::DoText(OpenBabel::CDXReader&)’: 2025-09-09T00:43:54,064 ./src/formats/chemdrawcdx.cpp:625:13: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:43:54,064 625 | ss >> text; 2025-09-09T00:43:54,064 | ^~~~ 2025-09-09T00:43:54,065 ./src/formats/chemdrawcdx.cpp:626:5: note: here 2025-09-09T00:43:54,065 626 | default: 2025-09-09T00:43:54,065 | ^~~~~~~ 2025-09-09T00:43:58,024 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2025-09-09T00:43:58,025 ./src/formats/chemdrawcdx.cpp:591:17: warning: ‘bgnIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:43:58,025 591 | if(!order || !bgnIdx || !endIdx) 2025-09-09T00:43:58,025 | ~~~~~~~^~~~~~~~~~ 2025-09-09T00:43:58,025 ./src/formats/chemdrawcdx.cpp:550:20: note: ‘bgnIdx’ was declared here 2025-09-09T00:43:58,025 550 | int order=1, bgnIdx, endIdx ; 2025-09-09T00:43:58,025 | ^~~~~~ 2025-09-09T00:43:58,026 ./src/formats/chemdrawcdx.cpp:591:28: warning: ‘endIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:43:58,026 591 | if(!order || !bgnIdx || !endIdx) 2025-09-09T00:43:58,026 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:43:58,026 ./src/formats/chemdrawcdx.cpp:550:28: note: ‘endIdx’ was declared here 2025-09-09T00:43:58,026 550 | int order=1, bgnIdx, endIdx ; 2025-09-09T00:43:58,026 | ^~~~~~ 2025-09-09T00:44:01,795 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawcdx.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:01,795 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/chemdrawcdx.o /tmp/ccevQthf.s 2025-09-09T00:44:01,800 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:02,707 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:44:02,707 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:44:02,707 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawcdx.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawcdx.' 2025-09-09T00:44:02,707 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/chemdrawct.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/chemdrawct.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:02,711 Using built-in specs. 2025-09-09T00:44:02,712 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:02,713 Target: arm-linux-gnueabihf 2025-09-09T00:44:02,713 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:44:02,713 Thread model: posix 2025-09-09T00:44:02,713 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:02,714 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:02,714 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawct.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:02,716 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemdrawct.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase chemdrawct.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cckSMsci.s 2025-09-09T00:44:02,728 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:02,728 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:44:02,729 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:02,729 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:02,730 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:02,730 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:02,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:02,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:02,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:02,731 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:02,732 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:02,732 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:02,732 #include "..." search starts here: 2025-09-09T00:44:02,732 #include <...> search starts here: 2025-09-09T00:44:02,732 /usr/include/eigen3 2025-09-09T00:44:02,733 include 2025-09-09T00:44:02,733 /usr/include/python3.13 2025-09-09T00:44:02,733 /usr/include/c++/14 2025-09-09T00:44:02,733 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:02,733 /usr/include/c++/14/backward 2025-09-09T00:44:02,734 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:02,734 /usr/local/include 2025-09-09T00:44:02,734 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:02,734 /usr/include 2025-09-09T00:44:02,734 End of search list. 2025-09-09T00:44:02,752 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:04,254 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:04,254 from include/openbabel/mol.h:43, 2025-09-09T00:44:04,254 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:04,254 from ./src/formats/chemdrawct.cpp:16: 2025-09-09T00:44:04,254 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:04,254 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:04,254 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:04,254 | ^ 2025-09-09T00:44:04,254 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:04,255 37 | # define UNUSED(x) x 2025-09-09T00:44:04,255 | ^ 2025-09-09T00:44:04,869 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:04,869 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:04,869 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:04,869 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:04,869 | ^ 2025-09-09T00:44:04,870 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:04,870 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:04,870 | ^~~~~~~~ 2025-09-09T00:44:04,874 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:04,874 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:04,874 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:04,874 | ^ 2025-09-09T00:44:04,874 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:04,874 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:04,875 | ^~~~~~~~ 2025-09-09T00:44:04,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:04,889 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:04,889 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:04,889 | ^ 2025-09-09T00:44:04,890 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:04,890 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:04,890 | ^~~~~~~~ 2025-09-09T00:44:04,895 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:04,895 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:04,895 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:04,895 | ^ 2025-09-09T00:44:04,895 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:04,895 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:04,895 | ^~~~~~~~ 2025-09-09T00:44:05,034 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:05,035 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:05,035 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:05,035 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:05,035 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:05,035 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:05,035 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:05,036 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:05,036 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:05,036 from include/openbabel/mol.h:35: 2025-09-09T00:44:05,036 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:05,036 131 | struct binary_function 2025-09-09T00:44:05,036 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:05,208 ./src/formats/chemdrawct.cpp: In member function ‘virtual bool OpenBabel::ChemDrawFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:44:05,208 ./src/formats/chemdrawct.cpp:130:22: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:44:05,208 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2025-09-09T00:44:05,208 | ~^ ~~~~~~~ 2025-09-09T00:44:05,208 | | | 2025-09-09T00:44:05,208 | int* unsigned int* 2025-09-09T00:44:05,208 | %d 2025-09-09T00:44:05,209 ./src/formats/chemdrawct.cpp:130:25: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:44:05,209 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2025-09-09T00:44:05,209 | ~^ ~~~~~~~ 2025-09-09T00:44:05,209 | | | 2025-09-09T00:44:05,209 | int* unsigned int* 2025-09-09T00:44:05,209 | %d 2025-09-09T00:44:05,211 ./src/formats/chemdrawct.cpp:153:32: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:44:05,211 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2025-09-09T00:44:05,211 | ~^ ~~~~ 2025-09-09T00:44:05,211 | | | 2025-09-09T00:44:05,211 | int* unsigned int* 2025-09-09T00:44:05,211 | %d 2025-09-09T00:44:05,212 ./src/formats/chemdrawct.cpp:153:34: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:44:05,212 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2025-09-09T00:44:05,212 | ~^ ~~~~ 2025-09-09T00:44:05,212 | | | 2025-09-09T00:44:05,212 | int* unsigned int* 2025-09-09T00:44:05,212 | %d 2025-09-09T00:44:05,212 ./src/formats/chemdrawct.cpp:153:36: warning: format ‘%d’ expects argument of type ‘int*’, but argument 5 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:44:05,213 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2025-09-09T00:44:05,213 | ~^ ~~~~~~ 2025-09-09T00:44:05,213 | | | 2025-09-09T00:44:05,213 | int* unsigned int* 2025-09-09T00:44:05,213 | %d 2025-09-09T00:44:07,297 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawct.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:07,298 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/chemdrawct.o /tmp/cckSMsci.s 2025-09-09T00:44:07,302 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:07,477 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:44:07,477 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:44:07,477 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawct.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/chemdrawct.' 2025-09-09T00:44:07,477 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/chemkinformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/chemkinformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:07,481 Using built-in specs. 2025-09-09T00:44:07,483 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:07,483 Target: arm-linux-gnueabihf 2025-09-09T00:44:07,483 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:44:07,483 Thread model: posix 2025-09-09T00:44:07,484 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:07,484 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:07,484 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemkinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:07,486 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemkinformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase chemkinformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccvrp7fw.s 2025-09-09T00:44:07,497 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:07,497 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:44:07,498 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:07,498 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:07,499 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:07,499 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:07,499 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:07,499 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:07,499 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:07,500 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:07,500 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:07,500 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:07,500 #include "..." search starts here: 2025-09-09T00:44:07,500 #include <...> search starts here: 2025-09-09T00:44:07,500 /usr/include/eigen3 2025-09-09T00:44:07,501 include 2025-09-09T00:44:07,501 /usr/include/python3.13 2025-09-09T00:44:07,501 /usr/include/c++/14 2025-09-09T00:44:07,501 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:07,501 /usr/include/c++/14/backward 2025-09-09T00:44:07,501 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:07,501 /usr/local/include 2025-09-09T00:44:07,502 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:07,502 /usr/include 2025-09-09T00:44:07,502 End of search list. 2025-09-09T00:44:07,522 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:09,186 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:09,186 from include/openbabel/mol.h:43, 2025-09-09T00:44:09,186 from ./src/formats/chemkinformat.cpp:25: 2025-09-09T00:44:09,186 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:09,186 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:09,186 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:09,186 | ^ 2025-09-09T00:44:09,186 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:09,187 37 | # define UNUSED(x) x 2025-09-09T00:44:09,187 | ^ 2025-09-09T00:44:09,801 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:09,801 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:09,801 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:09,801 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:09,801 | ^ 2025-09-09T00:44:09,802 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:09,802 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:09,802 | ^~~~~~~~ 2025-09-09T00:44:09,806 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:09,806 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:09,806 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:09,806 | ^ 2025-09-09T00:44:09,806 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:09,807 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:09,807 | ^~~~~~~~ 2025-09-09T00:44:09,823 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:09,823 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:09,823 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:09,823 | ^ 2025-09-09T00:44:09,823 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:09,823 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:09,824 | ^~~~~~~~ 2025-09-09T00:44:09,835 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:09,835 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:09,835 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:09,835 | ^ 2025-09-09T00:44:09,835 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:09,835 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:09,836 | ^~~~~~~~ 2025-09-09T00:44:09,972 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:09,972 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:09,972 from ./src/formats/chemkinformat.cpp:27: 2025-09-09T00:44:09,972 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:09,972 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:09,973 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:09,973 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:09,973 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:44:09,974 from ./src/formats/chemkinformat.cpp:18: 2025-09-09T00:44:09,974 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:09,974 131 | struct binary_function 2025-09-09T00:44:09,974 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:10,260 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:44:10,260 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:44:10,260 | ^~~~~~~~ 2025-09-09T00:44:10,261 In file included from ./src/formats/chemkinformat.cpp:28: 2025-09-09T00:44:10,261 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:44:10,261 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:44:10,261 | ^~~~~~~~ 2025-09-09T00:44:10,261 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:44:10,261 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:10,261 | ^~~~~~~~ 2025-09-09T00:44:10,262 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:44:10,262 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:44:10,262 | ^~~~~~~~ 2025-09-09T00:44:10,289 In file included from ./src/formats/chemkinformat.cpp:29: 2025-09-09T00:44:10,289 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:10,289 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:44:10,290 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2025-09-09T00:44:10,290 | ~~~~~~~~^~~~~~ 2025-09-09T00:44:10,305 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:10,305 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:44:10,305 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2025-09-09T00:44:10,306 | ~~~~~~~~^~~~~~ 2025-09-09T00:44:10,442 ./src/formats/chemkinformat.cpp: In member function ‘bool OpenBabel::ChemKinFormat::ReadReactionQualifierLines(std::istream&, OpenBabel::OBReaction*)’: 2025-09-09T00:44:10,442 ./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] 2025-09-09T00:44:10,442 634 | for(int i=0;iReactionType) 2025-09-09T00:44:10,526 | ^ 2025-09-09T00:44:10,526 ./src/formats/chemkinformat.cpp:905:11: warning: enumeration value ‘THREEBODY’ not handled in switch [-Wswitch] 2025-09-09T00:44:10,557 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘ARRHENIUS’ not handled in switch [-Wswitch] 2025-09-09T00:44:10,557 984 | switch(pRD->ReactionType) 2025-09-09T00:44:10,557 | ^ 2025-09-09T00:44:10,557 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘SRI’ not handled in switch [-Wswitch] 2025-09-09T00:44:23,764 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemkinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:23,765 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/chemkinformat.o /tmp/ccvrp7fw.s 2025-09-09T00:44:23,770 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:25,129 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:44:25,129 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:44:25,129 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemkinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/chemkinformat.' 2025-09-09T00:44:25,129 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/chemtoolformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/chemtoolformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:25,133 Using built-in specs. 2025-09-09T00:44:25,134 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:25,134 Target: arm-linux-gnueabihf 2025-09-09T00:44:25,134 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:44:25,134 Thread model: posix 2025-09-09T00:44:25,135 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:25,135 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:25,135 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemtoolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:25,135 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/chemtoolformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase chemtoolformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc4PpgPJ.s 2025-09-09T00:44:25,147 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:25,147 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:44:25,147 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:25,148 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:25,148 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:25,148 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:25,149 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:25,149 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:25,149 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:25,149 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:25,149 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:25,150 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:25,150 #include "..." search starts here: 2025-09-09T00:44:25,150 #include <...> search starts here: 2025-09-09T00:44:25,150 /usr/include/eigen3 2025-09-09T00:44:25,150 include 2025-09-09T00:44:25,150 /usr/include/python3.13 2025-09-09T00:44:25,151 /usr/include/c++/14 2025-09-09T00:44:25,151 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:25,151 /usr/include/c++/14/backward 2025-09-09T00:44:25,151 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:25,151 /usr/local/include 2025-09-09T00:44:25,151 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:25,151 /usr/include 2025-09-09T00:44:25,152 End of search list. 2025-09-09T00:44:25,168 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:26,675 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:26,675 from include/openbabel/mol.h:43, 2025-09-09T00:44:26,675 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:26,675 from ./src/formats/chemtoolformat.cpp:19: 2025-09-09T00:44:26,676 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:26,676 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:26,676 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:26,676 | ^ 2025-09-09T00:44:26,676 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:26,676 37 | # define UNUSED(x) x 2025-09-09T00:44:26,676 | ^ 2025-09-09T00:44:27,285 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:27,286 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:27,286 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:27,286 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:27,286 | ^ 2025-09-09T00:44:27,286 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:27,286 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:27,286 | ^~~~~~~~ 2025-09-09T00:44:27,289 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:27,289 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:27,289 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:27,290 | ^ 2025-09-09T00:44:27,290 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:27,290 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:27,290 | ^~~~~~~~ 2025-09-09T00:44:27,304 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:27,304 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:27,304 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:27,304 | ^ 2025-09-09T00:44:27,304 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:27,304 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:27,304 | ^~~~~~~~ 2025-09-09T00:44:27,309 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:27,309 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:27,309 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:27,309 | ^ 2025-09-09T00:44:27,309 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:27,309 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:27,309 | ^~~~~~~~ 2025-09-09T00:44:27,447 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:27,447 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:27,447 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:27,447 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:27,447 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:27,448 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:27,448 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:27,448 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:27,448 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:27,448 from include/openbabel/mol.h:35: 2025-09-09T00:44:27,448 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:27,448 131 | struct binary_function 2025-09-09T00:44:27,448 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:29,562 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemtoolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:29,562 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/chemtoolformat.o /tmp/cc4PpgPJ.s 2025-09-09T00:44:29,567 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:29,742 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:44:29,742 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:44:29,742 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/chemtoolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/chemtoolformat.' 2025-09-09T00:44:29,743 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/cifformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/cifformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:29,747 Using built-in specs. 2025-09-09T00:44:29,748 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:29,748 Target: arm-linux-gnueabihf 2025-09-09T00:44:29,748 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:44:29,748 Thread model: posix 2025-09-09T00:44:29,748 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:29,748 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:29,748 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:29,749 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cifformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase cifformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccHgqlGG.s 2025-09-09T00:44:29,759 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:29,759 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:44:29,760 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:29,760 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:29,760 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:29,760 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:29,760 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:29,760 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:29,760 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:29,760 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:29,761 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:29,761 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:29,761 #include "..." search starts here: 2025-09-09T00:44:29,761 #include <...> search starts here: 2025-09-09T00:44:29,761 /usr/include/eigen3 2025-09-09T00:44:29,761 include 2025-09-09T00:44:29,761 /usr/include/python3.13 2025-09-09T00:44:29,761 /usr/include/c++/14 2025-09-09T00:44:29,761 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:29,762 /usr/include/c++/14/backward 2025-09-09T00:44:29,762 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:29,762 /usr/local/include 2025-09-09T00:44:29,762 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:29,762 /usr/include 2025-09-09T00:44:29,762 End of search list. 2025-09-09T00:44:29,776 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:31,284 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:31,284 from include/openbabel/mol.h:43, 2025-09-09T00:44:31,284 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:31,284 from ./src/formats/cifformat.cpp:20: 2025-09-09T00:44:31,284 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:31,285 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:31,285 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:31,285 | ^ 2025-09-09T00:44:31,285 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:31,285 37 | # define UNUSED(x) x 2025-09-09T00:44:31,285 | ^ 2025-09-09T00:44:31,897 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:31,897 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:31,897 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:31,898 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:31,898 | ^ 2025-09-09T00:44:31,898 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:31,898 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:31,898 | ^~~~~~~~ 2025-09-09T00:44:31,901 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:31,901 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:31,901 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:31,901 | ^ 2025-09-09T00:44:31,902 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:31,902 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:31,902 | ^~~~~~~~ 2025-09-09T00:44:31,915 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:31,916 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:31,916 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:31,916 | ^ 2025-09-09T00:44:31,916 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:31,916 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:31,916 | ^~~~~~~~ 2025-09-09T00:44:31,920 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:31,921 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:31,921 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:31,921 | ^ 2025-09-09T00:44:31,921 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:31,921 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:31,921 | ^~~~~~~~ 2025-09-09T00:44:32,066 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:32,066 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:32,066 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:32,066 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:32,066 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:32,066 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:32,066 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:32,067 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:32,067 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:32,067 from include/openbabel/mol.h:35: 2025-09-09T00:44:32,067 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:32,067 131 | struct binary_function 2025-09-09T00:44:32,067 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:32,541 ./src/formats/cifformat.cpp: In member function ‘void OpenBabel::CIFData::CalcMatrices()’: 2025-09-09T00:44:32,541 ./src/formats/cifformat.cpp:900:11: warning: variable ‘aa’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:44:32,541 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:44:32,541 | ^~ 2025-09-09T00:44:32,541 ./src/formats/cifformat.cpp:900:14: warning: variable ‘bb’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:44:32,541 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:44:32,541 | ^~ 2025-09-09T00:44:32,541 ./src/formats/cifformat.cpp:900:27: warning: variable ‘betaa’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:44:32,541 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:44:32,541 | ^~~~~ 2025-09-09T00:44:32,542 ./src/formats/cifformat.cpp:900:33: warning: variable ‘gammaa’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:44:32,542 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:44:32,542 | ^~~~~~ 2025-09-09T00:44:37,660 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:44:37,660 from include/openbabel/mol.h:37: 2025-09-09T00:44:37,660 /usr/include/c++/14/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> >]’: 2025-09-09T00:44:37,660 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-09T00:44:37,661 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:44:37,661 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:41,034 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:44:41,034 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> >]’, 2025-09-09T00:44:41,034 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:876:39: 2025-09-09T00:44:41,034 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:44:41,034 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:44:41,034 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:41,035 514 | std::tuple(__k), 2025-09-09T00:44:41,035 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:41,035 515 | std::tuple<>()); 2025-09-09T00:44:41,035 | ~~~~~~~~~~~~~~~ 2025-09-09T00:44:41,036 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> >]’, 2025-09-09T00:44:41,036 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:887:37: 2025-09-09T00:44:41,036 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:44:41,036 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:44:41,036 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:41,037 514 | std::tuple(__k), 2025-09-09T00:44:41,037 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:41,037 515 | std::tuple<>()); 2025-09-09T00:44:41,037 | ~~~~~~~~~~~~~~~ 2025-09-09T00:44:47,301 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:47,302 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/cifformat.o /tmp/ccHgqlGG.s 2025-09-09T00:44:47,316 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:48,710 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:44:48,710 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:44:48,710 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/cifformat.' 2025-09-09T00:44:48,711 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/confabreport.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/confabreport.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:48,716 Using built-in specs. 2025-09-09T00:44:48,716 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:48,716 Target: arm-linux-gnueabihf 2025-09-09T00:44:48,716 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:44:48,716 Thread model: posix 2025-09-09T00:44:48,717 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:48,717 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:48,717 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/confabreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:48,717 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/confabreport.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase confabreport.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccHj4H2j.s 2025-09-09T00:44:48,728 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:48,728 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:44:48,728 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:48,729 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:48,730 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:48,730 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:48,730 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:48,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:48,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:48,731 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:48,731 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:48,731 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:48,731 #include "..." search starts here: 2025-09-09T00:44:48,731 #include <...> search starts here: 2025-09-09T00:44:48,732 /usr/include/eigen3 2025-09-09T00:44:48,732 include 2025-09-09T00:44:48,732 /usr/include/python3.13 2025-09-09T00:44:48,732 /usr/include/c++/14 2025-09-09T00:44:48,732 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:48,732 /usr/include/c++/14/backward 2025-09-09T00:44:48,732 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:48,732 /usr/local/include 2025-09-09T00:44:48,733 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:48,733 /usr/include 2025-09-09T00:44:48,733 End of search list. 2025-09-09T00:44:48,758 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:50,540 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:50,540 from include/openbabel/mol.h:43, 2025-09-09T00:44:50,540 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:50,540 from ./src/formats/confabreport.cpp:34: 2025-09-09T00:44:50,540 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:50,540 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:50,540 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:50,541 | ^ 2025-09-09T00:44:50,541 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:50,541 37 | # define UNUSED(x) x 2025-09-09T00:44:50,541 | ^ 2025-09-09T00:44:51,165 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:51,165 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:51,165 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:51,165 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:51,165 | ^ 2025-09-09T00:44:51,170 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:51,170 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:51,170 | ^~~~~~~~ 2025-09-09T00:44:51,170 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:51,170 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:51,170 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:51,170 | ^ 2025-09-09T00:44:51,170 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:51,171 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:51,171 | ^~~~~~~~ 2025-09-09T00:44:51,187 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:51,188 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:51,188 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:51,188 | ^ 2025-09-09T00:44:51,188 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:51,188 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:51,188 | ^~~~~~~~ 2025-09-09T00:44:51,190 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:51,190 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:51,190 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:51,190 | ^ 2025-09-09T00:44:51,190 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:51,190 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:51,190 | ^~~~~~~~ 2025-09-09T00:44:51,329 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:51,329 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:51,329 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:51,329 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:51,329 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:51,330 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:51,330 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:51,330 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:51,330 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:51,330 from include/openbabel/mol.h:35: 2025-09-09T00:44:51,330 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:51,330 131 | struct binary_function 2025-09-09T00:44:51,330 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:52,819 ./src/formats/confabreport.cpp: In member function ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’: 2025-09-09T00:44:52,819 ./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] 2025-09-09T00:44:52,819 128 | for (int i=1; i < binvals.size(); i++) 2025-09-09T00:44:52,819 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:44:52,821 ./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] 2025-09-09T00:44:52,821 133 | for (int i=1; i < cumbins.size(); i++) 2025-09-09T00:44:52,821 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:44:54,633 In file included from /usr/include/c++/14/bits/stl_algo.h:61, 2025-09-09T00:44:54,634 from /usr/include/c++/14/algorithm:61, 2025-09-09T00:44:54,634 from include/openbabel/ring.h:24, 2025-09-09T00:44:54,634 from include/openbabel/mol.h:51: 2025-09-09T00:44:54,634 /usr/include/c++/14/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]’: 2025-09-09T00:44:54,634 /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:54,634 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:44:54,634 | ^~~~~~~~~~~~~ 2025-09-09T00:44:54,675 /usr/include/c++/14/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]’: 2025-09-09T00:44:54,675 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:54,675 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:44:54,675 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:44:54,676 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:54,763 /usr/include/c++/14/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]’: 2025-09-09T00:44:54,763 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:54,763 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:44:54,763 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:44:54,763 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:54,764 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:54,764 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:44:54,764 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:55,348 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2025-09-09T00:44:55,349 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, 2025-09-09T00:44:55,349 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2025-09-09T00:44:55,349 /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:55,349 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:44:55,349 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:44:55,349 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:44:55,349 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:55,350 1907 | __comp); 2025-09-09T00:44:55,350 | ~~~~~~~ 2025-09-09T00:44:55,350 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2025-09-09T00:44:55,350 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++/14/bits/stl_algo.h:1908:31, 2025-09-09T00:44:55,350 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, 2025-09-09T00:44:55,350 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2025-09-09T00:44:55,350 /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:55,350 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:44:55,350 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:55,351 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:44:55,351 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:44:55,351 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:56,221 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/confabreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:56,221 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/confabreport.o /tmp/ccHj4H2j.s 2025-09-09T00:44:56,226 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:56,564 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:44:56,564 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:44:56,565 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/confabreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/confabreport.' 2025-09-09T00:44:56,567 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/copyformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/copyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:56,570 Using built-in specs. 2025-09-09T00:44:56,571 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:56,571 Target: arm-linux-gnueabihf 2025-09-09T00:44:56,572 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:44:56,572 Thread model: posix 2025-09-09T00:44:56,572 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:56,572 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:56,572 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/copyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:56,572 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/copyformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase copyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccPfGh12.s 2025-09-09T00:44:56,582 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:56,582 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:44:56,582 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:56,582 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:56,582 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:56,582 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:56,582 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:56,583 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:56,583 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:56,583 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:56,583 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:56,583 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:56,583 #include "..." search starts here: 2025-09-09T00:44:56,583 #include <...> search starts here: 2025-09-09T00:44:56,583 /usr/include/eigen3 2025-09-09T00:44:56,583 include 2025-09-09T00:44:56,583 /usr/include/python3.13 2025-09-09T00:44:56,584 /usr/include/c++/14 2025-09-09T00:44:56,584 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:56,584 /usr/include/c++/14/backward 2025-09-09T00:44:56,584 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:56,584 /usr/local/include 2025-09-09T00:44:56,584 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:56,584 /usr/include 2025-09-09T00:44:56,584 End of search list. 2025-09-09T00:44:56,600 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:57,928 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:57,928 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:57,929 from ./src/formats/copyformat.cpp:14: 2025-09-09T00:44:57,929 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:57,929 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:57,929 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:57,929 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:44:57,929 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:44:57,929 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:44:57,929 from /usr/include/c++/14/ios:44, 2025-09-09T00:44:57,929 from /usr/include/c++/14/ostream:40, 2025-09-09T00:44:57,930 from /usr/include/c++/14/iostream:41, 2025-09-09T00:44:57,930 from include/openbabel/obconversion.h:24: 2025-09-09T00:44:57,930 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:57,930 131 | struct binary_function 2025-09-09T00:44:57,930 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:58,657 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/copyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:58,657 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/copyformat.o /tmp/ccPfGh12.s 2025-09-09T00:44:58,670 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:58,734 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:44:58,734 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:44:58,734 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/copyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/copyformat.' 2025-09-09T00:44:58,735 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/crkformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/crkformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:58,740 Using built-in specs. 2025-09-09T00:44:58,740 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:58,740 Target: arm-linux-gnueabihf 2025-09-09T00:44:58,740 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:44:58,740 Thread model: posix 2025-09-09T00:44:58,740 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:58,740 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:58,741 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/crkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:44:58,741 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/crkformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase crkformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cczYobp4.s 2025-09-09T00:44:58,760 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:58,760 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:44:58,760 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:58,760 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:58,760 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:58,760 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:58,761 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:58,761 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:58,761 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:58,761 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:58,761 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:58,761 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:58,761 #include "..." search starts here: 2025-09-09T00:44:58,761 #include <...> search starts here: 2025-09-09T00:44:58,761 /usr/include/eigen3 2025-09-09T00:44:58,762 include 2025-09-09T00:44:58,762 /usr/include/python3.13 2025-09-09T00:44:58,762 /usr/include/c++/14 2025-09-09T00:44:58,762 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:58,762 /usr/include/c++/14/backward 2025-09-09T00:44:58,762 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:58,762 /usr/local/include 2025-09-09T00:44:58,762 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:58,762 /usr/include 2025-09-09T00:44:58,762 End of search list. 2025-09-09T00:44:58,770 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:00,280 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:00,280 from include/openbabel/mol.h:43, 2025-09-09T00:45:00,280 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:00,280 from ./src/formats/crkformat.cpp:16: 2025-09-09T00:45:00,280 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:00,280 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:00,280 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:00,280 | ^ 2025-09-09T00:45:00,281 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:00,281 37 | # define UNUSED(x) x 2025-09-09T00:45:00,281 | ^ 2025-09-09T00:45:00,890 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:00,890 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:00,890 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:00,890 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:00,890 | ^ 2025-09-09T00:45:00,890 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:00,890 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:00,890 | ^~~~~~~~ 2025-09-09T00:45:00,900 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:00,900 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:00,900 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:00,900 | ^ 2025-09-09T00:45:00,900 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:00,900 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:00,900 | ^~~~~~~~ 2025-09-09T00:45:00,907 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:00,907 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:00,907 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:00,907 | ^ 2025-09-09T00:45:00,908 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:00,908 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:00,908 | ^~~~~~~~ 2025-09-09T00:45:00,913 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:00,913 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:00,913 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:00,913 | ^ 2025-09-09T00:45:00,914 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:00,914 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:00,914 | ^~~~~~~~ 2025-09-09T00:45:01,052 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:01,052 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:01,052 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:01,052 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:01,052 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:01,052 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:01,052 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:01,053 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:01,053 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:01,054 from include/openbabel/mol.h:35: 2025-09-09T00:45:01,054 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:01,054 131 | struct binary_function 2025-09-09T00:45:01,054 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:04,552 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/crkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:04,553 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/crkformat.o /tmp/cczYobp4.s 2025-09-09T00:45:04,558 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:04,862 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:04,862 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:04,863 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/crkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/crkformat.' 2025-09-09T00:45:04,865 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/crystal09format.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/crystal09format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:04,868 Using built-in specs. 2025-09-09T00:45:04,870 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:04,870 Target: arm-linux-gnueabihf 2025-09-09T00:45:04,870 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:04,870 Thread model: posix 2025-09-09T00:45:04,870 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:04,871 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:04,871 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/crystal09format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:04,873 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/crystal09format.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase crystal09format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cch5IBUJ.s 2025-09-09T00:45:04,885 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:04,885 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:04,886 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:04,886 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:04,887 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:04,887 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:04,887 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:04,887 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:04,887 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:04,888 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:04,888 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:04,888 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:04,888 #include "..." search starts here: 2025-09-09T00:45:04,888 #include <...> search starts here: 2025-09-09T00:45:04,889 /usr/include/eigen3 2025-09-09T00:45:04,889 include 2025-09-09T00:45:04,889 /usr/include/python3.13 2025-09-09T00:45:04,889 /usr/include/c++/14 2025-09-09T00:45:04,889 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:04,889 /usr/include/c++/14/backward 2025-09-09T00:45:04,890 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:04,890 /usr/local/include 2025-09-09T00:45:04,890 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:04,890 /usr/include 2025-09-09T00:45:04,890 End of search list. 2025-09-09T00:45:04,906 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:06,483 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:06,483 from include/openbabel/mol.h:43, 2025-09-09T00:45:06,483 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:06,483 from ./src/formats/crystal09format.cpp:21: 2025-09-09T00:45:06,483 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:06,483 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:06,483 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:06,484 | ^ 2025-09-09T00:45:06,484 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:06,484 37 | # define UNUSED(x) x 2025-09-09T00:45:06,484 | ^ 2025-09-09T00:45:07,044 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:07,045 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:07,045 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:07,045 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:07,045 | ^ 2025-09-09T00:45:07,045 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:07,045 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:07,045 | ^~~~~~~~ 2025-09-09T00:45:07,049 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:07,049 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:07,050 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:07,050 | ^ 2025-09-09T00:45:07,050 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:07,050 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:07,050 | ^~~~~~~~ 2025-09-09T00:45:07,065 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:07,065 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:07,065 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:07,065 | ^ 2025-09-09T00:45:07,065 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:07,065 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:07,065 | ^~~~~~~~ 2025-09-09T00:45:07,070 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:07,071 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:07,071 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:07,071 | ^ 2025-09-09T00:45:07,071 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:07,071 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:07,071 | ^~~~~~~~ 2025-09-09T00:45:07,210 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:07,210 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:07,210 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:07,210 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:07,210 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:07,211 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:07,211 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:07,212 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:45:07,212 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:45:07,212 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:45:07,212 from /usr/include/c++/14/ios:44, 2025-09-09T00:45:07,212 from /usr/include/c++/14/istream:40, 2025-09-09T00:45:07,212 from /usr/include/c++/14/fstream:40, 2025-09-09T00:45:07,212 from ./src/formats/crystal09format.cpp:15: 2025-09-09T00:45:07,212 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:07,212 131 | struct binary_function 2025-09-09T00:45:07,212 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:12,644 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/crystal09format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:12,646 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/crystal09format.o /tmp/cch5IBUJ.s 2025-09-09T00:45:12,651 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:13,106 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:13,106 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:13,106 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/crystal09format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/crystal09format.' 2025-09-09T00:45:13,109 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/cssrformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/cssrformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:13,113 Using built-in specs. 2025-09-09T00:45:13,114 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:13,114 Target: arm-linux-gnueabihf 2025-09-09T00:45:13,115 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:13,115 Thread model: posix 2025-09-09T00:45:13,115 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:13,115 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:13,116 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cssrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:13,117 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/cssrformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase cssrformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc1WU1c8.s 2025-09-09T00:45:13,131 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:13,131 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:13,131 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:13,132 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:13,133 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:13,133 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:13,133 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:13,133 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:13,134 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:13,134 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:13,134 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:13,134 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:13,135 #include "..." search starts here: 2025-09-09T00:45:13,135 #include <...> search starts here: 2025-09-09T00:45:13,135 /usr/include/eigen3 2025-09-09T00:45:13,135 include 2025-09-09T00:45:13,135 /usr/include/python3.13 2025-09-09T00:45:13,136 /usr/include/c++/14 2025-09-09T00:45:13,136 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:13,136 /usr/include/c++/14/backward 2025-09-09T00:45:13,136 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:13,136 /usr/local/include 2025-09-09T00:45:13,137 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:13,137 /usr/include 2025-09-09T00:45:13,137 End of search list. 2025-09-09T00:45:13,157 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:14,655 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:14,655 from include/openbabel/mol.h:43, 2025-09-09T00:45:14,655 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:14,655 from ./src/formats/cssrformat.cpp:17: 2025-09-09T00:45:14,655 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:14,655 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:14,655 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:14,656 | ^ 2025-09-09T00:45:14,656 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:14,656 37 | # define UNUSED(x) x 2025-09-09T00:45:14,656 | ^ 2025-09-09T00:45:15,267 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:15,267 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:15,267 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:15,267 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:15,267 | ^ 2025-09-09T00:45:15,268 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:15,268 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:15,268 | ^~~~~~~~ 2025-09-09T00:45:15,272 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:15,272 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:15,272 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:15,272 | ^ 2025-09-09T00:45:15,272 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:15,273 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:15,273 | ^~~~~~~~ 2025-09-09T00:45:15,287 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:15,287 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:15,287 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:15,288 | ^ 2025-09-09T00:45:15,288 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:15,288 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:15,288 | ^~~~~~~~ 2025-09-09T00:45:15,293 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:15,293 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:15,293 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:15,294 | ^ 2025-09-09T00:45:15,294 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:15,294 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:15,294 | ^~~~~~~~ 2025-09-09T00:45:15,432 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:15,433 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:15,433 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:15,433 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:15,433 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:15,433 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:15,433 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:15,434 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:15,434 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:15,434 from include/openbabel/mol.h:35: 2025-09-09T00:45:15,434 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:15,434 131 | struct binary_function 2025-09-09T00:45:15,434 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:17,603 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cssrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:17,604 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/cssrformat.o /tmp/cc1WU1c8.s 2025-09-09T00:45:17,609 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:17,799 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:17,799 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:17,800 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/cssrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/cssrformat.' 2025-09-09T00:45:17,802 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/daltonformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/daltonformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:17,805 Using built-in specs. 2025-09-09T00:45:17,806 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:17,806 Target: arm-linux-gnueabihf 2025-09-09T00:45:17,806 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:17,807 Thread model: posix 2025-09-09T00:45:17,807 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:17,807 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:17,807 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/daltonformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:17,807 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/daltonformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase daltonformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccSPbQqp.s 2025-09-09T00:45:17,818 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:17,818 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:17,818 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:17,818 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:17,818 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:17,819 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:17,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:17,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:17,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:17,819 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:17,819 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:17,819 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:17,820 #include "..." search starts here: 2025-09-09T00:45:17,820 #include <...> search starts here: 2025-09-09T00:45:17,820 /usr/include/eigen3 2025-09-09T00:45:17,820 include 2025-09-09T00:45:17,820 /usr/include/python3.13 2025-09-09T00:45:17,820 /usr/include/c++/14 2025-09-09T00:45:17,820 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:17,820 /usr/include/c++/14/backward 2025-09-09T00:45:17,821 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:17,821 /usr/local/include 2025-09-09T00:45:17,821 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:17,821 /usr/include 2025-09-09T00:45:17,821 End of search list. 2025-09-09T00:45:17,837 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:19,338 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:19,339 from include/openbabel/mol.h:43, 2025-09-09T00:45:19,339 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:19,339 from ./src/formats/daltonformat.cpp:15: 2025-09-09T00:45:19,339 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:19,339 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:19,339 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:19,339 | ^ 2025-09-09T00:45:19,339 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:19,339 37 | # define UNUSED(x) x 2025-09-09T00:45:19,339 | ^ 2025-09-09T00:45:19,951 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:19,951 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:19,951 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:19,951 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:19,951 | ^ 2025-09-09T00:45:19,951 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:19,951 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:19,952 | ^~~~~~~~ 2025-09-09T00:45:19,954 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:19,955 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:19,955 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:19,955 | ^ 2025-09-09T00:45:19,955 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:19,955 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:19,955 | ^~~~~~~~ 2025-09-09T00:45:19,969 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:19,969 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:19,969 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:19,969 | ^ 2025-09-09T00:45:19,970 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:19,970 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:19,970 | ^~~~~~~~ 2025-09-09T00:45:19,975 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:19,975 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:19,975 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:19,975 | ^ 2025-09-09T00:45:19,975 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:19,975 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:19,976 | ^~~~~~~~ 2025-09-09T00:45:20,118 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:20,119 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:20,119 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:20,119 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:20,119 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:20,119 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:20,119 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:20,119 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:20,120 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:20,120 from include/openbabel/mol.h:35: 2025-09-09T00:45:20,120 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:20,120 131 | struct binary_function 2025-09-09T00:45:20,120 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:20,293 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:20,293 ./src/formats/daltonformat.cpp:142:9: warning: variable ‘atomcount’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:20,293 142 | int atomcount = 0; // for each atom type 2025-09-09T00:45:20,293 | ^~~~~~~~~ 2025-09-09T00:45:20,300 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:20,300 ./src/formats/daltonformat.cpp:306:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:45:20,300 306 | if(atom->GetAtomicNum() != atomtype) 2025-09-09T00:45:20,300 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:45:20,302 ./src/formats/daltonformat.cpp:326:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:45:20,303 326 | if(atom->GetAtomicNum() != atomtype) 2025-09-09T00:45:20,303 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:45:23,380 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/daltonformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:23,380 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/daltonformat.o /tmp/ccSPbQqp.s 2025-09-09T00:45:23,386 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:23,670 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:23,670 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:23,670 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/daltonformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/daltonformat.' 2025-09-09T00:45:23,672 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/dlpolyformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/dlpolyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:23,675 Using built-in specs. 2025-09-09T00:45:23,676 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:23,676 Target: arm-linux-gnueabihf 2025-09-09T00:45:23,676 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:23,676 Thread model: posix 2025-09-09T00:45:23,676 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:23,677 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:23,677 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/dlpolyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:23,677 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/dlpolyformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase dlpolyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccYTHnZz.s 2025-09-09T00:45:23,688 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:23,688 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:23,688 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:23,688 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:23,689 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:23,689 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:23,689 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:23,689 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:23,689 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:23,690 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:23,690 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:23,690 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:23,690 #include "..." search starts here: 2025-09-09T00:45:23,690 #include <...> search starts here: 2025-09-09T00:45:23,690 /usr/include/eigen3 2025-09-09T00:45:23,690 include 2025-09-09T00:45:23,690 /usr/include/python3.13 2025-09-09T00:45:23,691 /usr/include/c++/14 2025-09-09T00:45:23,691 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:23,691 /usr/include/c++/14/backward 2025-09-09T00:45:23,691 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:23,691 /usr/local/include 2025-09-09T00:45:23,691 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:23,691 /usr/include 2025-09-09T00:45:23,692 End of search list. 2025-09-09T00:45:23,709 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:25,233 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:25,233 from include/openbabel/mol.h:43, 2025-09-09T00:45:25,233 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:25,233 from ./src/formats/dlpolyformat.cpp:14: 2025-09-09T00:45:25,233 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:25,234 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:25,234 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:25,234 | ^ 2025-09-09T00:45:25,234 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:25,234 37 | # define UNUSED(x) x 2025-09-09T00:45:25,234 | ^ 2025-09-09T00:45:25,845 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:25,845 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:25,845 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:25,845 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:25,846 | ^ 2025-09-09T00:45:25,846 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:25,846 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:25,846 | ^~~~~~~~ 2025-09-09T00:45:25,849 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:25,849 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:25,849 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:25,849 | ^ 2025-09-09T00:45:25,849 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:25,850 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:25,850 | ^~~~~~~~ 2025-09-09T00:45:25,863 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:25,863 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:25,864 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:25,864 | ^ 2025-09-09T00:45:25,864 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:25,864 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:25,864 | ^~~~~~~~ 2025-09-09T00:45:25,868 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:25,868 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:25,869 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:25,869 | ^ 2025-09-09T00:45:25,869 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:25,869 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:25,869 | ^~~~~~~~ 2025-09-09T00:45:26,007 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:26,007 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:26,007 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:26,007 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:26,007 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:26,007 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:26,008 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:26,008 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:26,008 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:26,008 from include/openbabel/mol.h:35: 2025-09-09T00:45:26,008 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:26,008 131 | struct binary_function 2025-09-09T00:45:26,008 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:26,387 ./src/formats/dlpolyformat.cpp: In member function ‘bool OpenBabel::DlpolyInputReader::ParseUnitCell(std::istream&, OpenBabel::OBMol&)’: 2025-09-09T00:45:26,387 ./src/formats/dlpolyformat.cpp:147:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:26,388 147 | bool ok; 2025-09-09T00:45:26,388 | ^~ 2025-09-09T00:45:29,172 ./src/formats/dlpolyformat.cpp: In member function ‘virtual bool OpenBabel::DlpolyConfigFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:29,172 ./src/formats/dlpolyformat.cpp:370:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:45:29,172 370 | snprintf(buffer, BUFF_SIZE, "%20.15f %20.15f %20.15f\n", 2025-09-09T00:45:29,172 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,172 371 | atom->GetX(), 2025-09-09T00:45:29,172 | ~~~~~~~~~~~~~ 2025-09-09T00:45:29,172 372 | atom->GetY(), 2025-09-09T00:45:29,172 | ~~~~~~~~~~~~~ 2025-09-09T00:45:29,172 373 | atom->GetZ() 2025-09-09T00:45:29,173 | ~~~~~~~~~~~~ 2025-09-09T00:45:29,173 374 | ); 2025-09-09T00:45:29,173 | ~ 2025-09-09T00:45:34,506 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/dlpolyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:34,506 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/dlpolyformat.o /tmp/ccYTHnZz.s 2025-09-09T00:45:34,511 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:35,359 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:35,359 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:35,360 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/dlpolyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/dlpolyformat.' 2025-09-09T00:45:35,360 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/dmolformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/dmolformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:35,364 Using built-in specs. 2025-09-09T00:45:35,365 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:35,365 Target: arm-linux-gnueabihf 2025-09-09T00:45:35,366 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:35,366 Thread model: posix 2025-09-09T00:45:35,366 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:35,366 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:35,367 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/dmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:35,368 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/dmolformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase dmolformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccjBEmeA.s 2025-09-09T00:45:35,379 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:35,379 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:35,379 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:35,380 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:35,380 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:35,380 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:35,381 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:35,381 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:35,381 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:35,381 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:35,381 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:35,382 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:35,382 #include "..." search starts here: 2025-09-09T00:45:35,382 #include <...> search starts here: 2025-09-09T00:45:35,382 /usr/include/eigen3 2025-09-09T00:45:35,382 include 2025-09-09T00:45:35,382 /usr/include/python3.13 2025-09-09T00:45:35,383 /usr/include/c++/14 2025-09-09T00:45:35,383 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:35,383 /usr/include/c++/14/backward 2025-09-09T00:45:35,383 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:35,383 /usr/local/include 2025-09-09T00:45:35,384 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:35,384 /usr/include 2025-09-09T00:45:35,384 End of search list. 2025-09-09T00:45:35,404 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:36,916 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:36,916 from include/openbabel/mol.h:43, 2025-09-09T00:45:36,916 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:36,916 from ./src/formats/dmolformat.cpp:16: 2025-09-09T00:45:36,916 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:36,917 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:36,917 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:36,917 | ^ 2025-09-09T00:45:36,917 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:36,917 37 | # define UNUSED(x) x 2025-09-09T00:45:36,917 | ^ 2025-09-09T00:45:37,531 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:37,531 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:37,531 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:37,531 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:37,532 | ^ 2025-09-09T00:45:37,532 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:37,532 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:37,532 | ^~~~~~~~ 2025-09-09T00:45:37,536 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:37,536 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:37,536 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:37,536 | ^ 2025-09-09T00:45:37,536 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:37,537 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:37,537 | ^~~~~~~~ 2025-09-09T00:45:37,551 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:37,552 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:37,552 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:37,552 | ^ 2025-09-09T00:45:37,552 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:37,552 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:37,552 | ^~~~~~~~ 2025-09-09T00:45:37,557 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:37,557 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:37,558 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:37,558 | ^ 2025-09-09T00:45:37,558 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:37,558 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:37,558 | ^~~~~~~~ 2025-09-09T00:45:37,697 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:37,697 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:37,697 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:37,697 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:37,697 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:37,697 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:37,697 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:37,698 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:37,699 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:37,699 from include/openbabel/mol.h:35: 2025-09-09T00:45:37,699 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:37,699 131 | struct binary_function 2025-09-09T00:45:37,699 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:40,288 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/dmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:40,289 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/dmolformat.o /tmp/ccjBEmeA.s 2025-09-09T00:45:40,295 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:40,518 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:40,518 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:40,519 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/dmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/dmolformat.' 2025-09-09T00:45:40,521 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/exampleformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/exampleformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:40,525 Using built-in specs. 2025-09-09T00:45:40,526 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:40,526 Target: arm-linux-gnueabihf 2025-09-09T00:45:40,526 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:40,527 Thread model: posix 2025-09-09T00:45:40,527 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:40,527 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:40,527 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/exampleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:40,529 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/exampleformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase exampleformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccpq3CTr.s 2025-09-09T00:45:40,540 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:40,540 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:40,540 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:40,541 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:40,541 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:40,542 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:40,542 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:40,542 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:40,542 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:40,543 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:40,543 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:40,543 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:40,543 #include "..." search starts here: 2025-09-09T00:45:40,543 #include <...> search starts here: 2025-09-09T00:45:40,544 /usr/include/eigen3 2025-09-09T00:45:40,544 include 2025-09-09T00:45:40,544 /usr/include/python3.13 2025-09-09T00:45:40,544 /usr/include/c++/14 2025-09-09T00:45:40,544 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:40,544 /usr/include/c++/14/backward 2025-09-09T00:45:40,545 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:40,545 /usr/local/include 2025-09-09T00:45:40,545 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:40,545 /usr/include 2025-09-09T00:45:40,545 End of search list. 2025-09-09T00:45:40,567 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:41,018 ./src/formats/exampleformat.cpp:178:9: warning: "/*" within comment [-Wcomment] 2025-09-09T00:45:41,018 178 | /* Return true if ok. Returning false means discard the OBMol and stop 2025-09-09T00:45:42,068 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:42,068 from include/openbabel/mol.h:43, 2025-09-09T00:45:42,068 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:42,068 from ./src/formats/exampleformat.cpp:34: 2025-09-09T00:45:42,068 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:42,068 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:42,069 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:42,069 | ^ 2025-09-09T00:45:42,069 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:42,069 37 | # define UNUSED(x) x 2025-09-09T00:45:42,069 | ^ 2025-09-09T00:45:42,682 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:42,682 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:42,682 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:42,682 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:42,682 | ^ 2025-09-09T00:45:42,683 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:42,683 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:42,683 | ^~~~~~~~ 2025-09-09T00:45:42,687 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:42,687 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:42,687 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:42,687 | ^ 2025-09-09T00:45:42,687 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:42,687 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:42,688 | ^~~~~~~~ 2025-09-09T00:45:42,702 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:42,702 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:42,702 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:42,702 | ^ 2025-09-09T00:45:42,703 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:42,703 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:42,703 | ^~~~~~~~ 2025-09-09T00:45:42,708 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:42,708 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:42,708 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:42,708 | ^ 2025-09-09T00:45:42,709 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:42,709 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:42,709 | ^~~~~~~~ 2025-09-09T00:45:42,848 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:42,848 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:42,848 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:42,848 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:42,848 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:42,848 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:42,849 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:42,849 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:42,850 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:42,850 from include/openbabel/mol.h:35: 2025-09-09T00:45:42,850 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:42,850 131 | struct binary_function 2025-09-09T00:45:42,850 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:43,013 ./src/formats/exampleformat.cpp: In member function ‘virtual int OpenBabel::XXXFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:45:43,014 ./src/formats/exampleformat.cpp:128:37: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:45:43,014 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:45:43,014 | ~~~~^ 2025-09-09T00:45:43,014 ./src/formats/exampleformat.cpp:128:54: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:45:43,014 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:45:43,014 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:45:43,015 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:43,016 ./src/formats/exampleformat.cpp:156:12: warning: unused variable ‘ifs’ [-Wunused-variable] 2025-09-09T00:45:43,016 156 | istream& ifs = *pConv->GetInStream(); 2025-09-09T00:45:43,016 | ^~~ 2025-09-09T00:45:43,020 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:43,020 ./src/formats/exampleformat.cpp:203:13: warning: variable ‘levels’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:43,020 203 | int levels=0; 2025-09-09T00:45:43,020 | ^~~~~~ 2025-09-09T00:45:44,257 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:44,257 ./src/formats/exampleformat.cpp:171:27: warning: ‘dim’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:45:44,257 171 | pmol->SetDimension(dim); 2025-09-09T00:45:44,258 | ~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:45:44,258 ./src/formats/exampleformat.cpp:170:13: note: ‘dim’ was declared here 2025-09-09T00:45:44,258 170 | int dim; 2025-09-09T00:45:44,258 | ^~~ 2025-09-09T00:45:44,912 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/exampleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:44,912 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/exampleformat.o /tmp/ccpq3CTr.s 2025-09-09T00:45:44,917 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:45,076 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:45,076 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:45,076 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/exampleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/exampleformat.' 2025-09-09T00:45:45,077 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/exyzformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/exyzformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:45,081 Using built-in specs. 2025-09-09T00:45:45,082 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:45,082 Target: arm-linux-gnueabihf 2025-09-09T00:45:45,082 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:45,082 Thread model: posix 2025-09-09T00:45:45,082 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:45,082 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:45,082 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/exyzformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:45,083 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/exyzformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase exyzformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccHVhOmV.s 2025-09-09T00:45:45,092 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:45,092 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:45,092 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:45,092 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:45,092 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:45,092 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:45,093 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:45,093 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:45,093 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:45,093 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:45,093 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:45,093 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:45,093 #include "..." search starts here: 2025-09-09T00:45:45,094 #include <...> search starts here: 2025-09-09T00:45:45,094 /usr/include/eigen3 2025-09-09T00:45:45,094 include 2025-09-09T00:45:45,094 /usr/include/python3.13 2025-09-09T00:45:45,094 /usr/include/c++/14 2025-09-09T00:45:45,094 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:45,094 /usr/include/c++/14/backward 2025-09-09T00:45:45,094 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:45,095 /usr/local/include 2025-09-09T00:45:45,095 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:45,095 /usr/include 2025-09-09T00:45:45,095 End of search list. 2025-09-09T00:45:45,113 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:46,614 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:46,614 from include/openbabel/mol.h:43, 2025-09-09T00:45:46,614 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:46,614 from ./src/formats/exyzformat.cpp:18: 2025-09-09T00:45:46,614 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:46,614 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:46,614 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:46,614 | ^ 2025-09-09T00:45:46,615 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:46,615 37 | # define UNUSED(x) x 2025-09-09T00:45:46,615 | ^ 2025-09-09T00:45:47,225 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:47,225 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:47,225 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:47,225 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:47,225 | ^ 2025-09-09T00:45:47,225 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:47,225 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:47,225 | ^~~~~~~~ 2025-09-09T00:45:47,228 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:47,229 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:47,229 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:47,229 | ^ 2025-09-09T00:45:47,229 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:47,229 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:47,229 | ^~~~~~~~ 2025-09-09T00:45:47,243 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:47,243 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:47,243 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:47,243 | ^ 2025-09-09T00:45:47,243 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:47,244 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:47,244 | ^~~~~~~~ 2025-09-09T00:45:47,248 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:47,248 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:47,248 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:47,248 | ^ 2025-09-09T00:45:47,248 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:47,248 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:47,249 | ^~~~~~~~ 2025-09-09T00:45:47,386 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:47,386 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:47,386 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:47,386 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:47,386 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:47,387 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:47,387 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:47,387 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:47,387 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:47,387 from include/openbabel/mol.h:35: 2025-09-09T00:45:47,387 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:47,387 131 | struct binary_function 2025-09-09T00:45:47,387 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:47,710 ./src/formats/exyzformat.cpp: In member function ‘virtual bool OpenBabel::EXYZFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:47,710 ./src/formats/exyzformat.cpp:133:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:45:47,710 133 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2025-09-09T00:45:47,710 | ~^ ~~~~~~~ 2025-09-09T00:45:47,710 | | | 2025-09-09T00:45:47,710 | | unsigned int* 2025-09-09T00:45:47,710 | int* 2025-09-09T00:45:47,710 | %d 2025-09-09T00:45:47,767 ./src/formats/exyzformat.cpp:118:19: warning: variable ‘virtualAtoms’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:47,767 118 | bool unitCell,virtualAtoms; 2025-09-09T00:45:47,767 | ^~~~~~~~~~~~ 2025-09-09T00:45:52,691 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/exyzformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:52,693 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/exyzformat.o /tmp/ccHVhOmV.s 2025-09-09T00:45:52,700 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:53,125 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:53,125 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:53,125 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/exyzformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/exyzformat.' 2025-09-09T00:45:53,126 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/fastaformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fastaformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:53,130 Using built-in specs. 2025-09-09T00:45:53,131 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:53,131 Target: arm-linux-gnueabihf 2025-09-09T00:45:53,132 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:53,132 Thread model: posix 2025-09-09T00:45:53,132 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:53,132 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:53,132 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fastaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:53,134 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fastaformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase fastaformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccNw9YGM.s 2025-09-09T00:45:53,146 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:53,147 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:53,147 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:53,148 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:53,149 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:53,150 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:53,150 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:53,151 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:53,151 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:53,151 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:53,151 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:53,152 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:53,152 #include "..." search starts here: 2025-09-09T00:45:53,152 #include <...> search starts here: 2025-09-09T00:45:53,152 /usr/include/eigen3 2025-09-09T00:45:53,153 include 2025-09-09T00:45:53,153 /usr/include/python3.13 2025-09-09T00:45:53,153 /usr/include/c++/14 2025-09-09T00:45:53,153 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:53,153 /usr/include/c++/14/backward 2025-09-09T00:45:53,154 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:53,154 /usr/local/include 2025-09-09T00:45:53,154 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:53,154 /usr/include 2025-09-09T00:45:53,154 End of search list. 2025-09-09T00:45:53,173 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:54,723 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:54,724 from include/openbabel/mol.h:43, 2025-09-09T00:45:54,724 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:54,724 from ./src/formats/fastaformat.cpp:21: 2025-09-09T00:45:54,724 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:54,724 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:54,724 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:54,724 | ^ 2025-09-09T00:45:54,724 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:54,724 37 | # define UNUSED(x) x 2025-09-09T00:45:54,724 | ^ 2025-09-09T00:45:55,337 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:55,337 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:55,337 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:55,337 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:55,337 | ^ 2025-09-09T00:45:55,337 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:55,337 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:55,338 | ^~~~~~~~ 2025-09-09T00:45:55,341 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:55,342 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:55,342 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:55,342 | ^ 2025-09-09T00:45:55,342 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:55,342 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:55,342 | ^~~~~~~~ 2025-09-09T00:45:55,357 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:55,357 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:55,357 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:55,357 | ^ 2025-09-09T00:45:55,358 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:55,358 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:55,358 | ^~~~~~~~ 2025-09-09T00:45:55,363 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:55,363 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:55,363 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:55,363 | ^ 2025-09-09T00:45:55,363 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:55,364 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:55,364 | ^~~~~~~~ 2025-09-09T00:45:55,502 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:55,502 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:55,502 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:55,502 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:55,502 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:55,502 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:55,502 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:55,503 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:55,503 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:55,503 from include/openbabel/mol.h:35: 2025-09-09T00:45:55,503 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:55,504 131 | struct binary_function 2025-09-09T00:45:55,504 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:55,718 ./src/formats/fastaformat.cpp: In function ‘void OpenBabel::add_residue(OBMol*, OBResidue*, double, double, long unsigned int&, ResidueRecord*, int, OBAtom*&, bool, bool)’: 2025-09-09T00:45:55,719 ./src/formats/fastaformat.cpp:387:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-09T00:45:55,719 387 | else if (atom_count > resBondFromOffset) 2025-09-09T00:45:55,719 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:59,028 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fastaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:59,029 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/fastaformat.o /tmp/ccNw9YGM.s 2025-09-09T00:45:59,034 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:59,358 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:45:59,359 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:45:59,359 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fastaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/fastaformat.' 2025-09-09T00:45:59,361 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/fastsearchformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fastsearchformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:45:59,365 Using built-in specs. 2025-09-09T00:45:59,366 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:59,366 Target: arm-linux-gnueabihf 2025-09-09T00:45:59,366 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:45:59,367 Thread model: posix 2025-09-09T00:45:59,367 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:59,367 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:59,367 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fastsearchformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:45:59,369 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fastsearchformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase fastsearchformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccvSHBlY.s 2025-09-09T00:45:59,379 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:59,379 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:45:59,380 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:59,380 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:59,381 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:59,381 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:59,381 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:59,382 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:59,382 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:59,382 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:59,382 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:59,383 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:59,383 #include "..." search starts here: 2025-09-09T00:45:59,383 #include <...> search starts here: 2025-09-09T00:45:59,383 /usr/include/eigen3 2025-09-09T00:45:59,383 include 2025-09-09T00:45:59,384 /usr/include/python3.13 2025-09-09T00:45:59,384 /usr/include/c++/14 2025-09-09T00:45:59,384 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:59,384 /usr/include/c++/14/backward 2025-09-09T00:45:59,384 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:59,385 /usr/local/include 2025-09-09T00:45:59,385 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:59,385 /usr/include 2025-09-09T00:45:59,385 End of search list. 2025-09-09T00:45:59,406 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:00,885 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:00,885 from include/openbabel/mol.h:43, 2025-09-09T00:46:00,885 from ./src/formats/fastsearchformat.cpp:20: 2025-09-09T00:46:00,885 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:00,885 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:00,885 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:00,885 | ^ 2025-09-09T00:46:00,885 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:00,886 37 | # define UNUSED(x) x 2025-09-09T00:46:00,886 | ^ 2025-09-09T00:46:01,498 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:01,498 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:01,498 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:01,498 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:01,498 | ^ 2025-09-09T00:46:01,498 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:01,498 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:01,499 | ^~~~~~~~ 2025-09-09T00:46:01,502 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:01,503 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:01,503 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:01,503 | ^ 2025-09-09T00:46:01,503 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:01,503 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:01,503 | ^~~~~~~~ 2025-09-09T00:46:01,518 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:01,518 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:01,518 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:01,518 | ^ 2025-09-09T00:46:01,519 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:01,519 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:01,519 | ^~~~~~~~ 2025-09-09T00:46:01,524 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:01,524 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:01,524 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:01,524 | ^ 2025-09-09T00:46:01,524 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:01,524 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:01,525 | ^~~~~~~~ 2025-09-09T00:46:01,663 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:01,663 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:01,663 from ./src/formats/fastsearchformat.cpp:21: 2025-09-09T00:46:01,663 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:01,663 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:01,663 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:01,663 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:01,664 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:46:01,664 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:46:01,664 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:46:01,665 from /usr/include/c++/14/ios:44, 2025-09-09T00:46:01,665 from /usr/include/c++/14/istream:40, 2025-09-09T00:46:01,665 from /usr/include/c++/14/sstream:40, 2025-09-09T00:46:01,665 from ./src/formats/fastsearchformat.cpp:16: 2025-09-09T00:46:01,665 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:01,665 131 | struct binary_function 2025-09-09T00:46:01,665 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:01,893 ./src/formats/fastsearchformat.cpp: In member function ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’: 2025-09-09T00:46:01,893 ./src/formats/fastsearchformat.cpp:652:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:46:01,893 652 | if(idx>=patternMol.NumBonds()) 2025-09-09T00:46:01,893 | ~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:08,739 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fastsearchformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:08,739 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/fastsearchformat.o /tmp/ccvSHBlY.s 2025-09-09T00:46:08,745 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:09,420 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:09,420 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:09,420 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fastsearchformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/fastsearchformat.' 2025-09-09T00:46:09,423 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/fchkformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fchkformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:09,427 Using built-in specs. 2025-09-09T00:46:09,428 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:09,428 Target: arm-linux-gnueabihf 2025-09-09T00:46:09,429 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:09,429 Thread model: posix 2025-09-09T00:46:09,429 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:09,429 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:09,430 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fchkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:09,431 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fchkformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase fchkformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccht13fB.s 2025-09-09T00:46:09,442 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:09,443 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:09,443 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:09,443 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:09,444 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:09,445 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:09,445 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:09,445 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:09,446 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:09,446 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:09,446 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:09,446 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:09,447 #include "..." search starts here: 2025-09-09T00:46:09,447 #include <...> search starts here: 2025-09-09T00:46:09,447 /usr/include/eigen3 2025-09-09T00:46:09,447 include 2025-09-09T00:46:09,448 /usr/include/python3.13 2025-09-09T00:46:09,448 /usr/include/c++/14 2025-09-09T00:46:09,448 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:09,448 /usr/include/c++/14/backward 2025-09-09T00:46:09,448 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:09,448 /usr/local/include 2025-09-09T00:46:09,449 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:09,449 /usr/include 2025-09-09T00:46:09,449 End of search list. 2025-09-09T00:46:09,468 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:11,027 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:11,027 from include/openbabel/mol.h:43, 2025-09-09T00:46:11,027 from ./src/formats/fchkformat.cpp:21: 2025-09-09T00:46:11,028 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:11,028 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:11,028 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:11,028 | ^ 2025-09-09T00:46:11,028 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:11,028 37 | # define UNUSED(x) x 2025-09-09T00:46:11,028 | ^ 2025-09-09T00:46:11,643 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:11,644 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:11,644 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:11,644 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:11,644 | ^ 2025-09-09T00:46:11,644 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:11,644 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:11,644 | ^~~~~~~~ 2025-09-09T00:46:11,648 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:11,649 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:11,649 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:11,649 | ^ 2025-09-09T00:46:11,649 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:11,649 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:11,649 | ^~~~~~~~ 2025-09-09T00:46:11,664 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:11,664 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:11,664 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:11,664 | ^ 2025-09-09T00:46:11,665 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:11,665 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:11,665 | ^~~~~~~~ 2025-09-09T00:46:11,670 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:11,670 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:11,670 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:11,670 | ^ 2025-09-09T00:46:11,670 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:11,671 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:11,671 | ^~~~~~~~ 2025-09-09T00:46:11,809 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:11,810 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:11,810 from ./src/formats/fchkformat.cpp:22: 2025-09-09T00:46:11,810 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:11,810 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:11,810 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:11,810 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:11,811 In file included from /usr/include/c++/14/functional:49, 2025-09-09T00:46:11,811 from ./src/formats/fchkformat.cpp:16: 2025-09-09T00:46:11,811 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:11,811 131 | struct binary_function 2025-09-09T00:46:11,811 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:12,004 ./src/formats/fchkformat.cpp: In member function ‘virtual bool OpenBabel::FCHKFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:46:12,004 ./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] 2025-09-09T00:46:12,004 587 | if (alphaorb_found && (numAOrb > alphaorb.size())) 2025-09-09T00:46:12,005 | ~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:46:12,005 ./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] 2025-09-09T00:46:12,005 600 | if (betaorb_found && (numBOrb > betaorb.size())) 2025-09-09T00:46:12,005 | ~~~~~~~~^~~~~~~~~~~~~~~~ 2025-09-09T00:46:12,011 ./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] 2025-09-09T00:46:12,011 659 | bind2nd(less_equal(), 0)) || 2025-09-09T00:46:12,011 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:12,012 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:46:12,012 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:46:12,012 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:46:12,012 | ^~~~~~~ 2025-09-09T00:46:12,015 ./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] 2025-09-09T00:46:12,015 662 | bind2nd(greater(), MxBond)) || 2025-09-09T00:46:12,015 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:12,015 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:46:12,015 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:46:12,015 | ^~~~~~~ 2025-09-09T00:46:12,017 ./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] 2025-09-09T00:46:12,017 665 | bind2nd(less(), 0)) || 2025-09-09T00:46:12,017 | ~~~~~~~^~~~~~~~~~~~~~~~ 2025-09-09T00:46:12,018 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:46:12,018 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:46:12,018 | ^~~~~~~ 2025-09-09T00:46:12,026 ./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] 2025-09-09T00:46:12,026 668 | bind2nd(greater(), Natoms))) 2025-09-09T00:46:12,026 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:12,026 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:46:12,026 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:46:12,026 | ^~~~~~~ 2025-09-09T00:46:12,029 ./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] 2025-09-09T00:46:12,029 691 | if (numAOrb > 0 && alphaorb.size() == numAOrb) { 2025-09-09T00:46:12,029 | ~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:46:12,032 ./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] 2025-09-09T00:46:12,032 695 | if (numBOrb > 0 && betaorb.size() == numBOrb) { // open shell calculation 2025-09-09T00:46:12,032 | ~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:46:19,791 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fchkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:19,791 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/fchkformat.o /tmp/ccht13fB.s 2025-09-09T00:46:19,796 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:20,495 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:20,495 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:20,495 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fchkformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/fchkformat.' 2025-09-09T00:46:20,498 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/featformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/featformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:20,501 Using built-in specs. 2025-09-09T00:46:20,502 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:20,502 Target: arm-linux-gnueabihf 2025-09-09T00:46:20,502 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:20,502 Thread model: posix 2025-09-09T00:46:20,503 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:20,503 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:20,503 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/featformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:20,503 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/featformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase featformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccGExZ4U.s 2025-09-09T00:46:20,513 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:20,513 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:20,513 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:20,514 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:20,514 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:20,514 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:20,514 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:20,514 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:20,514 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:20,515 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:20,515 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:20,515 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:20,515 #include "..." search starts here: 2025-09-09T00:46:20,515 #include <...> search starts here: 2025-09-09T00:46:20,515 /usr/include/eigen3 2025-09-09T00:46:20,515 include 2025-09-09T00:46:20,516 /usr/include/python3.13 2025-09-09T00:46:20,516 /usr/include/c++/14 2025-09-09T00:46:20,516 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:20,516 /usr/include/c++/14/backward 2025-09-09T00:46:20,516 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:20,516 /usr/local/include 2025-09-09T00:46:20,516 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:20,516 /usr/include 2025-09-09T00:46:20,517 End of search list. 2025-09-09T00:46:20,534 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:22,029 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:22,029 from include/openbabel/mol.h:43, 2025-09-09T00:46:22,029 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:22,029 from ./src/formats/featformat.cpp:17: 2025-09-09T00:46:22,029 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:22,029 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:22,029 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:22,030 | ^ 2025-09-09T00:46:22,030 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:22,030 37 | # define UNUSED(x) x 2025-09-09T00:46:22,030 | ^ 2025-09-09T00:46:22,642 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:22,642 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:22,642 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:22,642 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:22,642 | ^ 2025-09-09T00:46:22,642 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:22,643 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:22,643 | ^~~~~~~~ 2025-09-09T00:46:22,646 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:22,646 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:22,646 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:22,646 | ^ 2025-09-09T00:46:22,646 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:22,646 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:22,646 | ^~~~~~~~ 2025-09-09T00:46:22,660 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:22,660 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:22,660 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:22,660 | ^ 2025-09-09T00:46:22,661 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:22,661 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:22,661 | ^~~~~~~~ 2025-09-09T00:46:22,665 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:22,665 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:22,665 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:22,665 | ^ 2025-09-09T00:46:22,666 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:22,666 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:22,666 | ^~~~~~~~ 2025-09-09T00:46:22,804 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:22,804 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:22,804 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:22,804 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:22,804 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:22,804 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:22,805 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:22,805 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:22,805 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:22,805 from include/openbabel/mol.h:35: 2025-09-09T00:46:22,805 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:22,805 131 | struct binary_function 2025-09-09T00:46:22,805 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:24,951 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/featformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:24,951 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/featformat.o /tmp/ccGExZ4U.s 2025-09-09T00:46:24,960 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:25,118 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:25,118 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:25,119 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/featformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/featformat.' 2025-09-09T00:46:25,119 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/fhformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fhformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:25,124 Using built-in specs. 2025-09-09T00:46:25,124 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:25,124 Target: arm-linux-gnueabihf 2025-09-09T00:46:25,125 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:25,125 Thread model: posix 2025-09-09T00:46:25,125 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:25,125 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:25,125 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fhformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:25,125 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fhformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase fhformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccliJveU.s 2025-09-09T00:46:25,135 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:25,136 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:25,136 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:25,136 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:25,136 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:25,136 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:25,136 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:25,137 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:25,137 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:25,137 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:25,137 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:25,137 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:25,137 #include "..." search starts here: 2025-09-09T00:46:25,138 #include <...> search starts here: 2025-09-09T00:46:25,138 /usr/include/eigen3 2025-09-09T00:46:25,138 include 2025-09-09T00:46:25,138 /usr/include/python3.13 2025-09-09T00:46:25,138 /usr/include/c++/14 2025-09-09T00:46:25,138 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:25,138 /usr/include/c++/14/backward 2025-09-09T00:46:25,138 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:25,139 /usr/local/include 2025-09-09T00:46:25,139 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:25,139 /usr/include 2025-09-09T00:46:25,139 End of search list. 2025-09-09T00:46:25,160 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:26,680 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:26,680 from include/openbabel/mol.h:43, 2025-09-09T00:46:26,680 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:26,680 from ./src/formats/fhformat.cpp:17: 2025-09-09T00:46:26,680 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:26,680 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:26,680 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:26,680 | ^ 2025-09-09T00:46:26,681 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:26,681 37 | # define UNUSED(x) x 2025-09-09T00:46:26,681 | ^ 2025-09-09T00:46:27,287 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:27,287 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:27,287 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:27,287 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:27,287 | ^ 2025-09-09T00:46:27,290 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:27,290 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:27,290 | ^~~~~~~~ 2025-09-09T00:46:27,300 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:27,300 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:27,300 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:27,300 | ^ 2025-09-09T00:46:27,300 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:27,300 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:27,300 | ^~~~~~~~ 2025-09-09T00:46:27,306 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:27,307 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:27,307 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:27,307 | ^ 2025-09-09T00:46:27,307 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:27,307 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:27,307 | ^~~~~~~~ 2025-09-09T00:46:27,312 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:27,313 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:27,313 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:27,313 | ^ 2025-09-09T00:46:27,313 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:27,313 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:27,313 | ^~~~~~~~ 2025-09-09T00:46:27,452 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:27,452 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:27,452 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:27,452 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:27,452 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:27,452 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:27,452 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:27,453 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:27,453 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:27,453 from include/openbabel/mol.h:35: 2025-09-09T00:46:27,453 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:27,454 131 | struct binary_function 2025-09-09T00:46:27,454 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:29,586 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fhformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:29,586 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/fhformat.o /tmp/ccliJveU.s 2025-09-09T00:46:29,590 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:29,760 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:29,760 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:29,760 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fhformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/fhformat.' 2025-09-09T00:46:29,761 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/fhiaimsformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fhiaimsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:29,765 Using built-in specs. 2025-09-09T00:46:29,766 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:29,766 Target: arm-linux-gnueabihf 2025-09-09T00:46:29,766 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:29,766 Thread model: posix 2025-09-09T00:46:29,767 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:29,767 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:29,767 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fhiaimsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:29,769 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fhiaimsformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase fhiaimsformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccOo7zAj.s 2025-09-09T00:46:29,779 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:29,779 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:29,779 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:29,780 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:29,780 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:29,780 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:29,781 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:29,781 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:29,781 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:29,781 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:29,781 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:29,781 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:29,782 #include "..." search starts here: 2025-09-09T00:46:29,782 #include <...> search starts here: 2025-09-09T00:46:29,782 /usr/include/eigen3 2025-09-09T00:46:29,782 include 2025-09-09T00:46:29,782 /usr/include/python3.13 2025-09-09T00:46:29,783 /usr/include/c++/14 2025-09-09T00:46:29,783 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:29,783 /usr/include/c++/14/backward 2025-09-09T00:46:29,783 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:29,783 /usr/local/include 2025-09-09T00:46:29,784 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:29,784 /usr/include 2025-09-09T00:46:29,784 End of search list. 2025-09-09T00:46:29,804 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:31,310 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:31,310 from include/openbabel/mol.h:43, 2025-09-09T00:46:31,310 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:31,311 from ./src/formats/fhiaimsformat.cpp:15: 2025-09-09T00:46:31,311 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:31,311 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:31,311 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:31,311 | ^ 2025-09-09T00:46:31,311 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:31,311 37 | # define UNUSED(x) x 2025-09-09T00:46:31,311 | ^ 2025-09-09T00:46:31,924 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:31,924 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:31,924 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:31,924 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:31,924 | ^ 2025-09-09T00:46:31,925 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:31,925 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:31,925 | ^~~~~~~~ 2025-09-09T00:46:31,929 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:31,929 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:31,929 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:31,929 | ^ 2025-09-09T00:46:31,929 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:31,929 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:31,929 | ^~~~~~~~ 2025-09-09T00:46:31,944 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:31,944 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:31,944 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:31,944 | ^ 2025-09-09T00:46:31,945 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:31,945 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:31,945 | ^~~~~~~~ 2025-09-09T00:46:31,950 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:31,950 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:31,950 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:31,950 | ^ 2025-09-09T00:46:31,951 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:31,951 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:31,951 | ^~~~~~~~ 2025-09-09T00:46:32,090 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:32,090 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:32,090 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:32,090 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:32,090 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:32,090 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:32,090 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:32,091 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:32,091 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:32,092 from include/openbabel/mol.h:35: 2025-09-09T00:46:32,092 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:32,092 131 | struct binary_function 2025-09-09T00:46:32,092 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:34,634 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fhiaimsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:34,635 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/fhiaimsformat.o /tmp/ccOo7zAj.s 2025-09-09T00:46:34,641 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:34,857 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:34,857 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:34,858 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fhiaimsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/fhiaimsformat.' 2025-09-09T00:46:34,860 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/fingerprintformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fingerprintformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:34,864 Using built-in specs. 2025-09-09T00:46:34,865 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:34,865 Target: arm-linux-gnueabihf 2025-09-09T00:46:34,866 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:34,866 Thread model: posix 2025-09-09T00:46:34,866 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:34,866 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:34,867 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fingerprintformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:34,868 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fingerprintformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase fingerprintformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccTwofUj.s 2025-09-09T00:46:34,879 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:34,880 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:34,880 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:34,880 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:34,881 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:34,881 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:34,881 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:34,881 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:34,882 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:34,882 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:34,882 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:34,882 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:34,882 #include "..." search starts here: 2025-09-09T00:46:34,883 #include <...> search starts here: 2025-09-09T00:46:34,883 /usr/include/eigen3 2025-09-09T00:46:34,883 include 2025-09-09T00:46:34,883 /usr/include/python3.13 2025-09-09T00:46:34,883 /usr/include/c++/14 2025-09-09T00:46:34,884 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:34,884 /usr/include/c++/14/backward 2025-09-09T00:46:34,884 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:34,884 /usr/local/include 2025-09-09T00:46:34,884 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:34,884 /usr/include 2025-09-09T00:46:34,885 End of search list. 2025-09-09T00:46:34,905 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:36,521 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:36,521 from include/openbabel/mol.h:43, 2025-09-09T00:46:36,521 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:36,521 from ./src/formats/fingerprintformat.cpp:19: 2025-09-09T00:46:36,521 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:36,521 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:36,521 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:36,521 | ^ 2025-09-09T00:46:36,521 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:36,522 37 | # define UNUSED(x) x 2025-09-09T00:46:36,522 | ^ 2025-09-09T00:46:37,137 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:37,137 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:37,137 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:37,137 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:37,137 | ^ 2025-09-09T00:46:37,137 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:37,137 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:37,138 | ^~~~~~~~ 2025-09-09T00:46:37,142 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:37,142 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:37,142 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:37,142 | ^ 2025-09-09T00:46:37,142 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:37,142 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:37,142 | ^~~~~~~~ 2025-09-09T00:46:37,157 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:37,157 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:37,157 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:37,157 | ^ 2025-09-09T00:46:37,158 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:37,158 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:37,158 | ^~~~~~~~ 2025-09-09T00:46:37,163 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:37,163 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:37,163 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:37,163 | ^ 2025-09-09T00:46:37,163 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:37,164 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:37,164 | ^~~~~~~~ 2025-09-09T00:46:37,302 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:37,302 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:37,302 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:37,303 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:37,303 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:37,303 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:37,303 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:37,304 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:37,304 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:37,304 from ./src/formats/fingerprintformat.cpp:15: 2025-09-09T00:46:37,304 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:37,304 131 | struct binary_function 2025-09-09T00:46:37,304 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:40,615 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fingerprintformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:40,616 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/fingerprintformat.o /tmp/ccTwofUj.s 2025-09-09T00:46:40,621 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:40,916 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:40,916 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:40,917 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fingerprintformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/fingerprintformat.' 2025-09-09T00:46:40,919 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/fpsformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fpsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:40,923 Using built-in specs. 2025-09-09T00:46:40,924 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:40,924 Target: arm-linux-gnueabihf 2025-09-09T00:46:40,924 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:40,924 Thread model: posix 2025-09-09T00:46:40,924 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:40,924 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:40,924 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fpsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:40,924 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/fpsformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase fpsformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccVzISHK.s 2025-09-09T00:46:40,934 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:40,934 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:40,934 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:40,934 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:40,935 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:40,935 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:40,935 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:40,935 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:40,935 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:40,935 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:40,935 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:40,935 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:40,935 #include "..." search starts here: 2025-09-09T00:46:40,935 #include <...> search starts here: 2025-09-09T00:46:40,936 /usr/include/eigen3 2025-09-09T00:46:40,936 include 2025-09-09T00:46:40,936 /usr/include/python3.13 2025-09-09T00:46:40,936 /usr/include/c++/14 2025-09-09T00:46:40,936 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:40,936 /usr/include/c++/14/backward 2025-09-09T00:46:40,936 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:40,936 /usr/local/include 2025-09-09T00:46:40,936 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:40,936 /usr/include 2025-09-09T00:46:40,936 End of search list. 2025-09-09T00:46:40,951 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:42,558 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:42,558 from include/openbabel/mol.h:43, 2025-09-09T00:46:42,558 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:42,558 from ./src/formats/fpsformat.cpp:19: 2025-09-09T00:46:42,558 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:42,558 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:42,558 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:42,559 | ^ 2025-09-09T00:46:42,559 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:42,559 37 | # define UNUSED(x) x 2025-09-09T00:46:42,559 | ^ 2025-09-09T00:46:43,172 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:43,172 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:43,172 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:43,173 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:43,173 | ^ 2025-09-09T00:46:43,173 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:43,173 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:43,173 | ^~~~~~~~ 2025-09-09T00:46:43,176 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:43,176 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:43,176 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:43,176 | ^ 2025-09-09T00:46:43,176 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:43,177 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:43,177 | ^~~~~~~~ 2025-09-09T00:46:43,190 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:43,191 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:43,191 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:43,191 | ^ 2025-09-09T00:46:43,191 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:43,191 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:43,191 | ^~~~~~~~ 2025-09-09T00:46:43,195 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:43,195 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:43,196 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:43,196 | ^ 2025-09-09T00:46:43,196 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:43,196 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:43,196 | ^~~~~~~~ 2025-09-09T00:46:43,334 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:43,334 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:43,334 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:43,334 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:43,334 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:43,335 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:43,335 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:43,335 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:43,335 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:43,335 from ./src/formats/fpsformat.cpp:15: 2025-09-09T00:46:43,335 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:43,335 131 | struct binary_function 2025-09-09T00:46:43,335 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:43,530 ./src/formats/fpsformat.cpp: In member function ‘virtual bool OpenBabel::FPSFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:46:43,530 ./src/formats/fpsformat.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:46:43,530 146 | for(unsigned i=0;i<(_nbits+31)/32;++i) 2025-09-09T00:46:43,530 | ~^~~~~~~~~~~~~~~ 2025-09-09T00:46:43,540 ./src/formats/fpsformat.cpp: In member function ‘std::string OpenBabel::FPSFormat::getTimeStr()’: 2025-09-09T00:46:43,540 ./src/formats/fpsformat.cpp:169:10: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:46:43,540 169 | size_t time_res; /* Result of strftime */ 2025-09-09T00:46:43,540 | ^~~~~~~~ 2025-09-09T00:46:46,381 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fpsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:46,382 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/fpsformat.o /tmp/ccVzISHK.s 2025-09-09T00:46:46,388 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:46,658 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:46,658 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:46,658 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/fpsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/fpsformat.' 2025-09-09T00:46:46,660 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/freefracformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/freefracformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:46,664 Using built-in specs. 2025-09-09T00:46:46,665 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:46,666 Target: arm-linux-gnueabihf 2025-09-09T00:46:46,666 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:46,666 Thread model: posix 2025-09-09T00:46:46,666 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:46,666 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:46,667 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/freefracformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:46,668 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/freefracformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase freefracformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc3oBPcd.s 2025-09-09T00:46:46,681 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:46,682 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:46,682 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:46,683 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:46,683 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:46,684 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:46,684 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:46,684 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:46,684 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:46,685 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:46,685 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:46,685 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:46,685 #include "..." search starts here: 2025-09-09T00:46:46,685 #include <...> search starts here: 2025-09-09T00:46:46,685 /usr/include/eigen3 2025-09-09T00:46:46,686 include 2025-09-09T00:46:46,686 /usr/include/python3.13 2025-09-09T00:46:46,686 /usr/include/c++/14 2025-09-09T00:46:46,686 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:46,686 /usr/include/c++/14/backward 2025-09-09T00:46:46,687 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:46,687 /usr/local/include 2025-09-09T00:46:46,687 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:46,687 /usr/include 2025-09-09T00:46:46,687 End of search list. 2025-09-09T00:46:46,707 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:48,215 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:48,215 from include/openbabel/mol.h:43, 2025-09-09T00:46:48,215 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:48,216 from ./src/formats/freefracformat.cpp:16: 2025-09-09T00:46:48,216 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:48,216 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:48,216 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:48,216 | ^ 2025-09-09T00:46:48,216 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:48,216 37 | # define UNUSED(x) x 2025-09-09T00:46:48,216 | ^ 2025-09-09T00:46:48,833 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:48,833 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:48,833 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:48,833 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:48,834 | ^ 2025-09-09T00:46:48,834 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:48,834 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:48,834 | ^~~~~~~~ 2025-09-09T00:46:48,838 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:48,838 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:48,838 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:48,838 | ^ 2025-09-09T00:46:48,839 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:48,839 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:48,839 | ^~~~~~~~ 2025-09-09T00:46:48,854 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:48,854 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:48,854 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:48,854 | ^ 2025-09-09T00:46:48,854 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:48,855 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:48,855 | ^~~~~~~~ 2025-09-09T00:46:48,860 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:48,861 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:48,861 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:48,861 | ^ 2025-09-09T00:46:48,861 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:48,861 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:48,861 | ^~~~~~~~ 2025-09-09T00:46:49,001 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:49,002 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:49,002 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:49,002 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:49,002 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:49,002 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:49,002 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:49,003 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:49,003 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:49,003 from include/openbabel/mol.h:35: 2025-09-09T00:46:49,003 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:49,003 131 | struct binary_function 2025-09-09T00:46:49,003 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:51,566 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/freefracformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:51,567 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/freefracformat.o /tmp/cc3oBPcd.s 2025-09-09T00:46:51,572 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:51,807 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:46:51,807 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:46:51,807 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/freefracformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/freefracformat.' 2025-09-09T00:46:51,809 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/gamessformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/gamessformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:51,813 Using built-in specs. 2025-09-09T00:46:51,814 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:51,814 Target: arm-linux-gnueabihf 2025-09-09T00:46:51,814 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:46:51,814 Thread model: posix 2025-09-09T00:46:51,814 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:51,814 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:51,814 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:46:51,815 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gamessformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase gamessformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc5vtiHE.s 2025-09-09T00:46:51,825 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:51,825 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:46:51,825 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:51,825 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:51,825 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:51,825 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:51,825 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:51,826 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:51,826 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:51,826 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:51,826 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:51,826 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:51,826 #include "..." search starts here: 2025-09-09T00:46:51,826 #include <...> search starts here: 2025-09-09T00:46:51,826 /usr/include/eigen3 2025-09-09T00:46:51,826 include 2025-09-09T00:46:51,827 /usr/include/python3.13 2025-09-09T00:46:51,827 /usr/include/c++/14 2025-09-09T00:46:51,827 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:51,827 /usr/include/c++/14/backward 2025-09-09T00:46:51,827 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:51,827 /usr/local/include 2025-09-09T00:46:51,827 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:51,827 /usr/include 2025-09-09T00:46:51,827 End of search list. 2025-09-09T00:46:51,841 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:53,351 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:53,351 from include/openbabel/mol.h:43, 2025-09-09T00:46:53,351 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:53,351 from ./src/formats/gamessformat.cpp:19: 2025-09-09T00:46:53,352 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:53,352 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:53,352 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:53,352 | ^ 2025-09-09T00:46:53,352 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:53,352 37 | # define UNUSED(x) x 2025-09-09T00:46:53,352 | ^ 2025-09-09T00:46:53,964 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:53,964 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:53,964 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:53,964 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:53,964 | ^ 2025-09-09T00:46:53,964 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:53,964 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:53,964 | ^~~~~~~~ 2025-09-09T00:46:53,967 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:53,968 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:53,968 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:53,968 | ^ 2025-09-09T00:46:53,968 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:53,968 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:53,968 | ^~~~~~~~ 2025-09-09T00:46:53,982 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:53,982 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:53,982 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:53,982 | ^ 2025-09-09T00:46:53,982 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:53,983 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:53,983 | ^~~~~~~~ 2025-09-09T00:46:53,987 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:53,987 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:53,987 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:53,987 | ^ 2025-09-09T00:46:53,987 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:53,988 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:53,988 | ^~~~~~~~ 2025-09-09T00:46:54,125 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:54,126 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:54,126 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:54,126 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:54,126 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:54,126 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:54,126 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:54,126 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:54,126 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:54,127 from include/openbabel/mol.h:35: 2025-09-09T00:46:54,127 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:54,127 131 | struct binary_function 2025-09-09T00:46:54,127 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:54,350 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:46:54,350 ./src/formats/gamessformat.cpp:227:9: warning: variable ‘ndummyatoms’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:46:54,350 227 | int ndummyatoms = 0; 2025-09-09T00:46:54,350 | ^~~~~~~~~~~ 2025-09-09T00:46:54,367 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:46:54,367 ./src/formats/gamessformat.cpp:995:14: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 2025-09-09T00:46:54,367 995 | static const bool cmpfn(const char& a, const char& b) { 2025-09-09T00:46:54,367 | ^~~~~ 2025-09-09T00:47:03,020 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:03,020 ./src/formats/gamessformat.cpp:510:11: warning: ‘lowFreqModesBegin’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:47:03,020 510 | if (numFreq < lowFreqModesBegin) // imaginary frequency 2025-09-09T00:47:03,021 | ^~ 2025-09-09T00:47:03,021 ./src/formats/gamessformat.cpp:238:9: note: ‘lowFreqModesBegin’ was declared here 2025-09-09T00:47:03,021 238 | int lowFreqModesBegin; // the number of the first low frequency mode 2025-09-09T00:47:03,021 | ^~~~~~~~~~~~~~~~~ 2025-09-09T00:47:03,024 ./src/formats/gamessformat.cpp:512:11: warning: ‘lowFreqModesEnd’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:47:03,024 512 | if (numFreq > lowFreqModesEnd) 2025-09-09T00:47:03,024 | ^~ 2025-09-09T00:47:03,024 ./src/formats/gamessformat.cpp:239:9: note: ‘lowFreqModesEnd’ was declared here 2025-09-09T00:47:03,024 239 | int lowFreqModesEnd; // the number of the last low frequency mode 2025-09-09T00:47:03,024 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:08,028 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:08,030 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/gamessformat.o /tmp/cc5vtiHE.s 2025-09-09T00:47:08,038 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:09,070 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:47:09,070 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:47:09,071 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessformat.' 2025-09-09T00:47:09,075 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/gamessukformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/gamessukformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:47:09,079 Using built-in specs. 2025-09-09T00:47:09,080 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:09,080 Target: arm-linux-gnueabihf 2025-09-09T00:47:09,081 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:47:09,081 Thread model: posix 2025-09-09T00:47:09,081 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:09,081 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:09,082 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessukformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:09,083 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gamessukformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase gamessukformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc4QvmYf.s 2025-09-09T00:47:09,096 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:09,097 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:47:09,097 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:09,098 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:09,099 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:09,100 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:09,100 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:09,100 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:09,101 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:09,101 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:09,101 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:09,101 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:09,101 #include "..." search starts here: 2025-09-09T00:47:09,102 #include <...> search starts here: 2025-09-09T00:47:09,102 /usr/include/eigen3 2025-09-09T00:47:09,102 include 2025-09-09T00:47:09,102 /usr/include/python3.13 2025-09-09T00:47:09,102 /usr/include/c++/14 2025-09-09T00:47:09,102 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:09,102 /usr/include/c++/14/backward 2025-09-09T00:47:09,102 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:09,103 /usr/local/include 2025-09-09T00:47:09,103 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:09,103 /usr/include 2025-09-09T00:47:09,103 End of search list. 2025-09-09T00:47:09,119 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:47:10,632 In file included from include/openbabel/atom.h:33, 2025-09-09T00:47:10,632 from include/openbabel/mol.h:43, 2025-09-09T00:47:10,632 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:47:10,632 from ./src/formats/gamessukformat.cpp:14: 2025-09-09T00:47:10,632 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:47:10,632 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:47:10,632 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:47:10,633 | ^ 2025-09-09T00:47:10,633 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:47:10,633 37 | # define UNUSED(x) x 2025-09-09T00:47:10,633 | ^ 2025-09-09T00:47:11,244 In file included from include/openbabel/mol.h:52: 2025-09-09T00:47:11,244 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:11,244 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:11,244 862 | {return new OBVibrationData(*this);} 2025-09-09T00:47:11,244 | ^ 2025-09-09T00:47:11,244 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:47:11,244 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:47:11,245 | ^~~~~~~~ 2025-09-09T00:47:11,249 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:11,249 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:11,249 907 | {return new OBDOSData(*this);} 2025-09-09T00:47:11,249 | ^ 2025-09-09T00:47:11,249 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:47:11,249 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:47:11,249 | ^~~~~~~~ 2025-09-09T00:47:11,264 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:11,264 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:11,264 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:47:11,264 | ^ 2025-09-09T00:47:11,265 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:47:11,265 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:47:11,265 | ^~~~~~~~ 2025-09-09T00:47:11,270 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:11,270 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:11,270 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:47:11,270 | ^ 2025-09-09T00:47:11,270 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:47:11,271 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:47:11,271 | ^~~~~~~~ 2025-09-09T00:47:11,409 In file included from include/openbabel/format.h:22, 2025-09-09T00:47:11,409 from include/openbabel/obconversion.h:37, 2025-09-09T00:47:11,409 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:47:11,409 include/openbabel/plugin.h: At global scope: 2025-09-09T00:47:11,410 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:47:11,410 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:47:11,410 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:11,410 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:47:11,410 from /usr/include/c++/14/vector:68, 2025-09-09T00:47:11,410 from include/openbabel/mol.h:35: 2025-09-09T00:47:11,411 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:47:11,411 131 | struct binary_function 2025-09-09T00:47:11,411 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:11,630 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’: 2025-09-09T00:47:11,630 ./src/formats/gamessukformat.cpp:307:97: warning: unused parameter ‘factor’ [-Wunused-parameter] 2025-09-09T00:47:11,630 307 | bool GAMESSUKFormat::ReadLineZmatrix(OBMol &mol, OBAtom *atom, vector &tokens, double factor, int *zmatLineCount) 2025-09-09T00:47:11,630 | ~~~~~~~^~~~~~ 2025-09-09T00:47:11,669 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadInitialCartesian(OpenBabel::OBMol&, std::istream&)’: 2025-09-09T00:47:11,669 ./src/formats/gamessukformat.cpp:779:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:47:11,670 779 | bool ok=false; 2025-09-09T00:47:11,670 | ^~ 2025-09-09T00:47:11,672 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz1(OpenBabel::OBMol&, std::istream&)’: 2025-09-09T00:47:11,672 ./src/formats/gamessukformat.cpp:845:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:47:11,672 845 | bool ok=false; 2025-09-09T00:47:11,672 | ^~ 2025-09-09T00:47:11,675 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz2(OpenBabel::OBMol&, std::istream&)’: 2025-09-09T00:47:11,675 ./src/formats/gamessukformat.cpp:892:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:47:11,675 892 | bool ok=false; 2025-09-09T00:47:11,675 | ^~ 2025-09-09T00:47:11,701 ./src/formats/gamessukformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSUKOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:11,701 ./src/formats/gamessukformat.cpp:1207:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:47:11,701 1207 | bool ok; 2025-09-09T00:47:11,701 | ^~ 2025-09-09T00:47:15,066 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:47:15,066 from include/openbabel/mol.h:37: 2025-09-09T00:47:15,066 /usr/include/c++/14/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> >]’: 2025-09-09T00:47:15,066 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-09T00:47:15,066 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:47:15,067 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:16,728 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:47:16,728 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> >]’, 2025-09-09T00:47:16,728 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadVariables(std::istream&, double, std::string)’ at ./src/formats/gamessukformat.cpp:472:26: 2025-09-09T00:47:16,729 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:16,729 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:16,729 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:16,729 514 | std::tuple(__k), 2025-09-09T00:47:16,729 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:16,729 515 | std::tuple<>()); 2025-09-09T00:47:16,729 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,182 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> >]’, 2025-09-09T00:47:18,182 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:280:32: 2025-09-09T00:47:18,182 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:18,182 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:18,182 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,182 514 | std::tuple(__k), 2025-09-09T00:47:18,182 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,183 515 | std::tuple<>()); 2025-09-09T00:47:18,183 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,184 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> >]’, 2025-09-09T00:47:18,185 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:288:32: 2025-09-09T00:47:18,185 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:18,185 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:18,185 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,185 514 | std::tuple(__k), 2025-09-09T00:47:18,185 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,185 515 | std::tuple<>()); 2025-09-09T00:47:18,185 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,187 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> >]’, 2025-09-09T00:47:18,187 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:296:32: 2025-09-09T00:47:18,187 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:18,187 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:18,188 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,188 514 | std::tuple(__k), 2025-09-09T00:47:18,188 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,188 515 | std::tuple<>()); 2025-09-09T00:47:18,188 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,856 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> >]’, 2025-09-09T00:47:19,857 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:339:36: 2025-09-09T00:47:19,857 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:19,857 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:19,857 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,857 514 | std::tuple(__k), 2025-09-09T00:47:19,857 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,857 515 | std::tuple<>()); 2025-09-09T00:47:19,857 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,859 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> >]’, 2025-09-09T00:47:19,859 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:357:36: 2025-09-09T00:47:19,860 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:19,860 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:19,860 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,860 514 | std::tuple(__k), 2025-09-09T00:47:19,860 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,860 515 | std::tuple<>()); 2025-09-09T00:47:19,860 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,862 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> >]’, 2025-09-09T00:47:19,862 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:370:36: 2025-09-09T00:47:19,862 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:19,862 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:19,863 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,863 514 | std::tuple(__k), 2025-09-09T00:47:19,863 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,863 515 | std::tuple<>()); 2025-09-09T00:47:19,863 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,866 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> >]’, 2025-09-09T00:47:19,866 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:386:36: 2025-09-09T00:47:19,867 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:19,867 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:19,867 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,867 514 | std::tuple(__k), 2025-09-09T00:47:19,867 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,867 515 | std::tuple<>()); 2025-09-09T00:47:19,867 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,869 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> >]’, 2025-09-09T00:47:19,869 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:398:36: 2025-09-09T00:47:19,869 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:19,869 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:19,870 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,870 514 | std::tuple(__k), 2025-09-09T00:47:19,870 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,870 515 | std::tuple<>()); 2025-09-09T00:47:19,870 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,872 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> >]’, 2025-09-09T00:47:19,872 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:410:36: 2025-09-09T00:47:19,872 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:47:19,872 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:19,872 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,872 514 | std::tuple(__k), 2025-09-09T00:47:19,873 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:19,873 515 | std::tuple<>()); 2025-09-09T00:47:19,873 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:24,728 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessukformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:24,728 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/gamessukformat.o /tmp/cc4QvmYf.s 2025-09-09T00:47:24,733 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:25,990 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:47:25,990 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:47:25,990 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessukformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/gamessukformat.' 2025-09-09T00:47:25,991 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/gausscubeformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/gausscubeformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:47:25,995 Using built-in specs. 2025-09-09T00:47:25,996 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:25,996 Target: arm-linux-gnueabihf 2025-09-09T00:47:25,996 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:47:25,996 Thread model: posix 2025-09-09T00:47:25,996 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:25,997 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:25,997 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gausscubeformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:25,997 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gausscubeformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase gausscubeformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cci2vd4V.s 2025-09-09T00:47:26,007 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:26,008 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:47:26,008 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:26,008 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:26,008 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:26,008 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:26,009 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:26,009 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:26,009 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:26,009 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:26,009 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:26,009 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:26,009 #include "..." search starts here: 2025-09-09T00:47:26,009 #include <...> search starts here: 2025-09-09T00:47:26,010 /usr/include/eigen3 2025-09-09T00:47:26,010 include 2025-09-09T00:47:26,010 /usr/include/python3.13 2025-09-09T00:47:26,010 /usr/include/c++/14 2025-09-09T00:47:26,010 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:26,010 /usr/include/c++/14/backward 2025-09-09T00:47:26,010 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:26,010 /usr/local/include 2025-09-09T00:47:26,010 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:26,010 /usr/include 2025-09-09T00:47:26,011 End of search list. 2025-09-09T00:47:26,025 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:47:27,517 In file included from include/openbabel/atom.h:33, 2025-09-09T00:47:27,518 from include/openbabel/mol.h:43, 2025-09-09T00:47:27,518 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:47:27,518 from ./src/formats/gausscubeformat.cpp:28: 2025-09-09T00:47:27,518 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:47:27,518 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:47:27,518 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:47:27,518 | ^ 2025-09-09T00:47:27,518 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:47:27,519 37 | # define UNUSED(x) x 2025-09-09T00:47:27,519 | ^ 2025-09-09T00:47:28,130 In file included from include/openbabel/mol.h:52: 2025-09-09T00:47:28,130 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:28,131 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:28,131 862 | {return new OBVibrationData(*this);} 2025-09-09T00:47:28,131 | ^ 2025-09-09T00:47:28,131 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:47:28,131 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:47:28,131 | ^~~~~~~~ 2025-09-09T00:47:28,134 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:28,134 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:28,134 907 | {return new OBDOSData(*this);} 2025-09-09T00:47:28,134 | ^ 2025-09-09T00:47:28,135 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:47:28,135 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:47:28,135 | ^~~~~~~~ 2025-09-09T00:47:28,149 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:28,149 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:28,149 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:47:28,149 | ^ 2025-09-09T00:47:28,149 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:47:28,149 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:47:28,149 | ^~~~~~~~ 2025-09-09T00:47:28,154 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:28,154 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:28,154 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:47:28,154 | ^ 2025-09-09T00:47:28,154 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:47:28,154 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:47:28,154 | ^~~~~~~~ 2025-09-09T00:47:28,292 In file included from include/openbabel/format.h:22, 2025-09-09T00:47:28,292 from include/openbabel/obconversion.h:37, 2025-09-09T00:47:28,293 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:47:28,293 include/openbabel/plugin.h: At global scope: 2025-09-09T00:47:28,293 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:47:28,293 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:47:28,293 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:28,293 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:47:28,293 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:47:28,293 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:47:28,293 from /usr/include/c++/14/ios:44, 2025-09-09T00:47:28,294 from /usr/include/c++/14/istream:40, 2025-09-09T00:47:28,294 from /usr/include/c++/14/sstream:40, 2025-09-09T00:47:28,294 from ./src/formats/gausscubeformat.cpp:25: 2025-09-09T00:47:28,294 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:47:28,294 131 | struct binary_function 2025-09-09T00:47:28,294 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:28,455 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:47:28,455 229 | virtual const std::string &GetValue() const 2025-09-09T00:47:28,455 | ^~~~~~~~ 2025-09-09T00:47:28,455 In file included from ./src/formats/gausscubeformat.cpp:29: 2025-09-09T00:47:28,456 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:47:28,456 76 | double GetValue (vector3 pos) const; 2025-09-09T00:47:28,456 | ^~~~~~~~ 2025-09-09T00:47:28,457 ./src/formats/gausscubeformat.cpp: In member function ‘virtual int OpenBabel::OBGaussianCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:47:28,458 ./src/formats/gausscubeformat.cpp:79:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:47:28,458 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:47:28,458 | ~~~~^ 2025-09-09T00:47:28,458 ./src/formats/gausscubeformat.cpp:79:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:28,458 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:47:28,458 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:28,526 ./src/formats/gausscubeformat.cpp: In member function ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:28,527 ./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] 2025-09-09T00:47:28,527 425 | while (vgd.size() < nCubes) 2025-09-09T00:47:28,527 | ~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:47:28,535 ./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] 2025-09-09T00:47:28,535 472 | while (values.size() < n*nCubes) 2025-09-09T00:47:28,535 | ~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:47:28,553 ./src/formats/gausscubeformat.cpp:107:17: warning: unused variable ‘title’ [-Wunused-variable] 2025-09-09T00:47:28,553 107 | const char* title = pConv->GetTitle(); 2025-09-09T00:47:28,553 | ^~~~~ 2025-09-09T00:47:36,262 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gausscubeformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:36,263 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/gausscubeformat.o /tmp/cci2vd4V.s 2025-09-09T00:47:36,268 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:36,871 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:47:36,871 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:47:36,871 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gausscubeformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/gausscubeformat.' 2025-09-09T00:47:36,874 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/gaussformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/gaussformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:47:36,878 Using built-in specs. 2025-09-09T00:47:36,878 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:36,879 Target: arm-linux-gnueabihf 2025-09-09T00:47:36,879 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:47:36,879 Thread model: posix 2025-09-09T00:47:36,879 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:36,879 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:36,879 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gaussformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:36,879 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gaussformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase gaussformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc4wkcCI.s 2025-09-09T00:47:36,891 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:36,892 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:47:36,892 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:36,892 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:36,892 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:36,892 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:36,892 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:36,892 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:36,893 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:36,893 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:36,893 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:36,893 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:36,893 #include "..." search starts here: 2025-09-09T00:47:36,893 #include <...> search starts here: 2025-09-09T00:47:36,893 /usr/include/eigen3 2025-09-09T00:47:36,894 include 2025-09-09T00:47:36,894 /usr/include/python3.13 2025-09-09T00:47:36,894 /usr/include/c++/14 2025-09-09T00:47:36,894 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:36,894 /usr/include/c++/14/backward 2025-09-09T00:47:36,894 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:36,894 /usr/local/include 2025-09-09T00:47:36,894 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:36,895 /usr/include 2025-09-09T00:47:36,895 End of search list. 2025-09-09T00:47:36,911 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:47:38,465 In file included from include/openbabel/atom.h:33, 2025-09-09T00:47:38,465 from include/openbabel/mol.h:43, 2025-09-09T00:47:38,466 from include/openbabel/data_utilities.h:25, 2025-09-09T00:47:38,466 from ./src/formats/gaussformat.cpp:18: 2025-09-09T00:47:38,466 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:47:38,466 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:47:38,466 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:47:38,466 | ^ 2025-09-09T00:47:38,466 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:47:38,466 37 | # define UNUSED(x) x 2025-09-09T00:47:38,466 | ^ 2025-09-09T00:47:39,005 In file included from include/openbabel/mol.h:52: 2025-09-09T00:47:39,005 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:39,005 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:39,006 862 | {return new OBVibrationData(*this);} 2025-09-09T00:47:39,006 | ^ 2025-09-09T00:47:39,006 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:47:39,006 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:47:39,006 | ^~~~~~~~ 2025-09-09T00:47:39,009 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:39,009 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:39,009 907 | {return new OBDOSData(*this);} 2025-09-09T00:47:39,009 | ^ 2025-09-09T00:47:39,010 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:47:39,010 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:47:39,010 | ^~~~~~~~ 2025-09-09T00:47:39,023 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:39,024 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:39,024 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:47:39,024 | ^ 2025-09-09T00:47:39,024 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:47:39,024 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:47:39,024 | ^~~~~~~~ 2025-09-09T00:47:39,028 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:39,028 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:39,029 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:47:39,029 | ^ 2025-09-09T00:47:39,029 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:47:39,029 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:47:39,029 | ^~~~~~~~ 2025-09-09T00:47:39,167 In file included from include/openbabel/format.h:22, 2025-09-09T00:47:39,167 from include/openbabel/obconversion.h:37, 2025-09-09T00:47:39,167 from include/openbabel/obmolecformat.h:31, 2025-09-09T00:47:39,167 from ./src/formats/gaussformat.cpp:19: 2025-09-09T00:47:39,167 include/openbabel/plugin.h: At global scope: 2025-09-09T00:47:39,168 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:47:39,168 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:47:39,168 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:39,168 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:47:39,168 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:47:39,168 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:47:39,168 from /usr/include/c++/14/ios:44, 2025-09-09T00:47:39,168 from /usr/include/c++/14/istream:40, 2025-09-09T00:47:39,168 from /usr/include/c++/14/fstream:40, 2025-09-09T00:47:39,169 from include/openbabel/data.h:27, 2025-09-09T00:47:39,169 from ./src/formats/gaussformat.cpp:17: 2025-09-09T00:47:39,169 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:47:39,169 131 | struct binary_function 2025-09-09T00:47:39,169 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:39,364 ./src/formats/gaussformat.cpp: In function ‘void OpenBabel::add_unique_pairdata_to_mol(OBMol*, std::string, std::string, int)’: 2025-09-09T00:47:39,365 ./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] 2025-09-09T00:47:39,365 275 | if (vs.size() >= start) 2025-09-09T00:47:39,365 | ~~~~~~~~~~^~~~~~~~ 2025-09-09T00:47:39,365 ./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] 2025-09-09T00:47:39,365 278 | for(i=start+1; (i)’: 2025-09-09T00:47:39,372 ./src/formats/gaussformat.cpp:332:17: warning: unused variable ‘pg’ [-Wunused-variable] 2025-09-09T00:47:39,372 332 | const char *pg = obPG.IdentifyPointGroup(); 2025-09-09T00:47:39,372 | ^~ 2025-09-09T00:47:57,216 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gaussformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:57,216 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/gaussformat.o /tmp/cc4wkcCI.s 2025-09-09T00:47:57,221 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:58,557 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:47:58,557 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:47:58,557 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gaussformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/gaussformat.' 2025-09-09T00:47:58,558 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/gausszmatformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/gausszmatformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:47:58,562 Using built-in specs. 2025-09-09T00:47:58,563 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:58,563 Target: arm-linux-gnueabihf 2025-09-09T00:47:58,563 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:47:58,563 Thread model: posix 2025-09-09T00:47:58,563 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:58,563 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:58,564 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gausszmatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:47:58,564 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gausszmatformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase gausszmatformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccyJ4ZU3.s 2025-09-09T00:47:58,575 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:58,575 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:47:58,575 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:58,576 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:58,576 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:58,576 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:58,576 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:58,576 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:58,576 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:58,576 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:58,577 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:58,577 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:58,577 #include "..." search starts here: 2025-09-09T00:47:58,577 #include <...> search starts here: 2025-09-09T00:47:58,577 /usr/include/eigen3 2025-09-09T00:47:58,577 include 2025-09-09T00:47:58,577 /usr/include/python3.13 2025-09-09T00:47:58,577 /usr/include/c++/14 2025-09-09T00:47:58,577 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:58,578 /usr/include/c++/14/backward 2025-09-09T00:47:58,578 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:58,578 /usr/local/include 2025-09-09T00:47:58,578 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:58,578 /usr/include 2025-09-09T00:47:58,578 End of search list. 2025-09-09T00:47:58,593 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:00,097 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:00,097 from include/openbabel/mol.h:43, 2025-09-09T00:48:00,097 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:00,097 from ./src/formats/gausszmatformat.cpp:16: 2025-09-09T00:48:00,097 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:00,097 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:00,098 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:00,098 | ^ 2025-09-09T00:48:00,098 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:00,098 37 | # define UNUSED(x) x 2025-09-09T00:48:00,098 | ^ 2025-09-09T00:48:00,709 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:00,709 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:00,709 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:00,709 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:00,710 | ^ 2025-09-09T00:48:00,710 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:00,710 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:00,710 | ^~~~~~~~ 2025-09-09T00:48:00,713 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:00,713 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:00,713 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:00,713 | ^ 2025-09-09T00:48:00,713 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:00,714 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:00,714 | ^~~~~~~~ 2025-09-09T00:48:00,727 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:00,728 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:00,728 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:00,728 | ^ 2025-09-09T00:48:00,728 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:00,728 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:00,728 | ^~~~~~~~ 2025-09-09T00:48:00,732 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:00,733 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:00,733 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:00,733 | ^ 2025-09-09T00:48:00,733 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:00,733 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:00,733 | ^~~~~~~~ 2025-09-09T00:48:00,872 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:00,873 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:00,873 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:00,873 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:00,873 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:00,873 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:00,873 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:00,873 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:00,873 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:00,874 from include/openbabel/mol.h:35: 2025-09-09T00:48:00,874 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:00,874 131 | struct binary_function 2025-09-09T00:48:00,874 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:03,069 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:48:03,069 from include/openbabel/mol.h:37: 2025-09-09T00:48:03,069 /usr/include/c++/14/bits/stl_tree.h: In 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> >]’: 2025-09-09T00:48:03,070 /usr/include/c++/14/bits/stl_tree.h:2208:5: 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 2025-09-09T00:48:03,070 2208 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:48:03,070 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:05,788 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gausszmatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:05,788 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/gausszmatformat.o /tmp/ccyJ4ZU3.s 2025-09-09T00:48:05,793 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:06,198 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:06,198 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:06,198 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gausszmatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/gausszmatformat.' 2025-09-09T00:48:06,200 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/genbankformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/genbankformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:06,204 Using built-in specs. 2025-09-09T00:48:06,205 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:06,205 Target: arm-linux-gnueabihf 2025-09-09T00:48:06,205 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:06,205 Thread model: posix 2025-09-09T00:48:06,205 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:06,205 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:06,205 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/genbankformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:06,206 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/genbankformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase genbankformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccBM61wz.s 2025-09-09T00:48:06,216 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:06,216 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:06,216 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:06,216 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:06,216 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:06,217 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:06,217 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:06,217 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:06,217 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:06,217 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:06,217 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:06,217 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:06,217 #include "..." search starts here: 2025-09-09T00:48:06,217 #include <...> search starts here: 2025-09-09T00:48:06,218 /usr/include/eigen3 2025-09-09T00:48:06,218 include 2025-09-09T00:48:06,218 /usr/include/python3.13 2025-09-09T00:48:06,218 /usr/include/c++/14 2025-09-09T00:48:06,218 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:06,218 /usr/include/c++/14/backward 2025-09-09T00:48:06,218 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:06,218 /usr/local/include 2025-09-09T00:48:06,218 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:06,218 /usr/include 2025-09-09T00:48:06,218 End of search list. 2025-09-09T00:48:06,233 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:07,743 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:07,743 from include/openbabel/mol.h:43, 2025-09-09T00:48:07,743 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:07,743 from ./src/formats/genbankformat.cpp:19: 2025-09-09T00:48:07,743 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:07,743 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:07,744 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:07,744 | ^ 2025-09-09T00:48:07,744 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:07,744 37 | # define UNUSED(x) x 2025-09-09T00:48:07,744 | ^ 2025-09-09T00:48:08,355 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:08,355 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:08,356 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:08,356 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:08,356 | ^ 2025-09-09T00:48:08,356 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:08,356 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:08,356 | ^~~~~~~~ 2025-09-09T00:48:08,359 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:08,359 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:08,359 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:08,360 | ^ 2025-09-09T00:48:08,360 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:08,360 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:08,360 | ^~~~~~~~ 2025-09-09T00:48:08,374 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:08,374 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:08,374 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:08,374 | ^ 2025-09-09T00:48:08,374 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:08,374 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:08,374 | ^~~~~~~~ 2025-09-09T00:48:08,379 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:08,379 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:08,379 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:08,379 | ^ 2025-09-09T00:48:08,379 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:08,379 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:08,379 | ^~~~~~~~ 2025-09-09T00:48:08,517 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:08,517 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:08,517 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:08,518 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:08,518 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:08,518 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:08,518 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:08,518 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:08,518 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:08,518 from include/openbabel/mol.h:35: 2025-09-09T00:48:08,518 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:08,518 131 | struct binary_function 2025-09-09T00:48:08,519 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:10,631 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/genbankformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:10,633 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/genbankformat.o /tmp/ccBM61wz.s 2025-09-09T00:48:10,641 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:10,801 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:10,801 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:10,801 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/genbankformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/genbankformat.' 2025-09-09T00:48:10,803 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/ghemicalformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/ghemicalformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:10,808 Using built-in specs. 2025-09-09T00:48:10,808 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:10,808 Target: arm-linux-gnueabihf 2025-09-09T00:48:10,809 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:10,809 Thread model: posix 2025-09-09T00:48:10,809 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:10,809 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:10,809 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/ghemicalformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:10,809 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/ghemicalformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase ghemicalformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc0jJ0wf.s 2025-09-09T00:48:10,820 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:10,820 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:10,820 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:10,820 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:10,821 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:10,830 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:10,830 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:10,830 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:10,830 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:10,830 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:10,830 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:10,831 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:10,831 #include "..." search starts here: 2025-09-09T00:48:10,831 #include <...> search starts here: 2025-09-09T00:48:10,831 /usr/include/eigen3 2025-09-09T00:48:10,831 include 2025-09-09T00:48:10,831 /usr/include/python3.13 2025-09-09T00:48:10,831 /usr/include/c++/14 2025-09-09T00:48:10,832 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:10,832 /usr/include/c++/14/backward 2025-09-09T00:48:10,832 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:10,832 /usr/local/include 2025-09-09T00:48:10,832 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:10,832 /usr/include 2025-09-09T00:48:10,832 End of search list. 2025-09-09T00:48:10,850 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:12,352 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:12,353 from include/openbabel/mol.h:43, 2025-09-09T00:48:12,353 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:12,353 from ./src/formats/ghemicalformat.cpp:17: 2025-09-09T00:48:12,353 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:12,353 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:12,353 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:12,353 | ^ 2025-09-09T00:48:12,353 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:12,354 37 | # define UNUSED(x) x 2025-09-09T00:48:12,354 | ^ 2025-09-09T00:48:12,963 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:12,963 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:12,964 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:12,964 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:12,964 | ^ 2025-09-09T00:48:12,964 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:12,964 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:12,964 | ^~~~~~~~ 2025-09-09T00:48:12,967 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:12,967 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:12,967 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:12,968 | ^ 2025-09-09T00:48:12,968 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:12,968 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:12,968 | ^~~~~~~~ 2025-09-09T00:48:12,981 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:12,982 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:12,982 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:12,982 | ^ 2025-09-09T00:48:12,982 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:12,982 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:12,982 | ^~~~~~~~ 2025-09-09T00:48:12,986 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:12,987 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:12,987 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:12,987 | ^ 2025-09-09T00:48:12,987 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:12,987 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:12,987 | ^~~~~~~~ 2025-09-09T00:48:13,127 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:13,127 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:13,127 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:13,127 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:13,127 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:13,127 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:13,127 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:13,128 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:13,128 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:13,128 from include/openbabel/mol.h:35: 2025-09-09T00:48:13,128 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:13,128 131 | struct binary_function 2025-09-09T00:48:13,128 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:15,924 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/ghemicalformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:15,924 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/ghemicalformat.o /tmp/cc0jJ0wf.s 2025-09-09T00:48:15,929 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:16,157 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:16,157 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:16,157 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/ghemicalformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/ghemicalformat.' 2025-09-09T00:48:16,158 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/groformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/groformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:16,162 Using built-in specs. 2025-09-09T00:48:16,163 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:16,163 Target: arm-linux-gnueabihf 2025-09-09T00:48:16,163 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:16,163 Thread model: posix 2025-09-09T00:48:16,163 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:16,163 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:16,163 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/groformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:16,164 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/groformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase groformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccXdiRpC.s 2025-09-09T00:48:16,173 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:16,173 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:16,173 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:16,173 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:16,174 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:16,174 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:16,174 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:16,174 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:16,174 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:16,174 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:16,174 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:16,174 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:16,175 #include "..." search starts here: 2025-09-09T00:48:16,175 #include <...> search starts here: 2025-09-09T00:48:16,175 /usr/include/eigen3 2025-09-09T00:48:16,175 include 2025-09-09T00:48:16,175 /usr/include/python3.13 2025-09-09T00:48:16,175 /usr/include/c++/14 2025-09-09T00:48:16,175 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:16,175 /usr/include/c++/14/backward 2025-09-09T00:48:16,176 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:16,176 /usr/local/include 2025-09-09T00:48:16,176 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:16,176 /usr/include 2025-09-09T00:48:16,176 End of search list. 2025-09-09T00:48:16,194 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:17,698 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:17,698 from include/openbabel/mol.h:43, 2025-09-09T00:48:17,698 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:17,698 from ./src/formats/groformat.cpp:16: 2025-09-09T00:48:17,698 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:17,699 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:17,699 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:17,699 | ^ 2025-09-09T00:48:17,699 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:17,699 37 | # define UNUSED(x) x 2025-09-09T00:48:17,699 | ^ 2025-09-09T00:48:18,309 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:18,309 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:18,309 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:18,309 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:18,309 | ^ 2025-09-09T00:48:18,310 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:18,310 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:18,310 | ^~~~~~~~ 2025-09-09T00:48:18,313 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:18,313 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:18,313 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:18,313 | ^ 2025-09-09T00:48:18,313 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:18,313 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:18,313 | ^~~~~~~~ 2025-09-09T00:48:18,327 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:18,327 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:18,327 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:18,328 | ^ 2025-09-09T00:48:18,328 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:18,328 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:18,328 | ^~~~~~~~ 2025-09-09T00:48:18,332 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:18,332 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:18,332 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:18,333 | ^ 2025-09-09T00:48:18,333 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:18,333 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:18,333 | ^~~~~~~~ 2025-09-09T00:48:18,471 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:18,471 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:18,471 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:18,471 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:18,471 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:18,471 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:18,472 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:18,472 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:18,472 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:18,472 from include/openbabel/mol.h:35: 2025-09-09T00:48:18,472 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:18,472 131 | struct binary_function 2025-09-09T00:48:18,472 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:22,073 ./src/formats/groformat.cpp: In member function ‘virtual bool OpenBabel::GROFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:22,073 ./src/formats/groformat.cpp:273:19: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:48:22,073 273 | res->AddAtom(atom); 2025-09-09T00:48:22,073 | ~~~~~~~~~~~~^~~~~~ 2025-09-09T00:48:22,073 ./src/formats/groformat.cpp:163:14: note: ‘res’ was declared here 2025-09-09T00:48:22,073 163 | OBResidue* res; 2025-09-09T00:48:22,073 | ^~~ 2025-09-09T00:48:23,987 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/groformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:23,987 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/groformat.o /tmp/ccXdiRpC.s 2025-09-09T00:48:23,992 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:24,431 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:24,432 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:24,432 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/groformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/groformat.' 2025-09-09T00:48:24,434 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/gromos96format.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/gromos96format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:24,438 Using built-in specs. 2025-09-09T00:48:24,438 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:24,438 Target: arm-linux-gnueabihf 2025-09-09T00:48:24,439 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:24,439 Thread model: posix 2025-09-09T00:48:24,439 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:24,439 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:24,439 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gromos96format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:24,439 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gromos96format.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase gromos96format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccV2ON3C.s 2025-09-09T00:48:24,449 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:24,449 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:24,449 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:24,449 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:24,449 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:24,449 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:24,450 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:24,450 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:24,450 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:24,450 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:24,450 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:24,450 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:24,450 #include "..." search starts here: 2025-09-09T00:48:24,450 #include <...> search starts here: 2025-09-09T00:48:24,450 /usr/include/eigen3 2025-09-09T00:48:24,450 include 2025-09-09T00:48:24,451 /usr/include/python3.13 2025-09-09T00:48:24,451 /usr/include/c++/14 2025-09-09T00:48:24,451 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:24,451 /usr/include/c++/14/backward 2025-09-09T00:48:24,451 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:24,451 /usr/local/include 2025-09-09T00:48:24,451 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:24,451 /usr/include 2025-09-09T00:48:24,451 End of search list. 2025-09-09T00:48:24,467 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:25,970 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:25,970 from include/openbabel/mol.h:43, 2025-09-09T00:48:25,971 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:25,971 from ./src/formats/gromos96format.cpp:54: 2025-09-09T00:48:25,971 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:25,971 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:25,971 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:25,971 | ^ 2025-09-09T00:48:25,971 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:25,971 37 | # define UNUSED(x) x 2025-09-09T00:48:25,971 | ^ 2025-09-09T00:48:26,586 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:26,586 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:26,587 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:26,587 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:26,587 | ^ 2025-09-09T00:48:26,587 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:26,587 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:26,587 | ^~~~~~~~ 2025-09-09T00:48:26,590 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:26,590 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:26,590 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:26,590 | ^ 2025-09-09T00:48:26,591 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:26,591 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:26,591 | ^~~~~~~~ 2025-09-09T00:48:26,604 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:26,605 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:26,605 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:26,605 | ^ 2025-09-09T00:48:26,605 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:26,605 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:26,605 | ^~~~~~~~ 2025-09-09T00:48:26,610 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:26,610 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:26,610 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:26,610 | ^ 2025-09-09T00:48:26,610 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:26,610 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:26,610 | ^~~~~~~~ 2025-09-09T00:48:26,748 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:26,749 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:26,749 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:26,749 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:26,749 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:26,749 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:26,749 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:26,749 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:26,749 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:26,749 from include/openbabel/mol.h:35: 2025-09-09T00:48:26,750 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:26,750 131 | struct binary_function 2025-09-09T00:48:26,750 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:28,325 ./src/formats/gromos96format.cpp: In member function ‘virtual bool OpenBabel::GROMOS96Format::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:28,326 ./src/formats/gromos96format.cpp:140:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2025-09-09T00:48:28,326 140 | strncpy(type_name,etab.GetSymbol(atom->GetAtomicNum()), 16); 2025-09-09T00:48:28,326 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:28,326 ./src/formats/gromos96format.cpp:132:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2025-09-09T00:48:28,326 132 | strncpy(res_name,(char*)res->GetName().c_str(), 16); 2025-09-09T00:48:28,326 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:28,326 ./src/formats/gromos96format.cpp:134:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2025-09-09T00:48:28,326 134 | strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16); 2025-09-09T00:48:28,327 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:28,823 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gromos96format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:28,823 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/gromos96format.o /tmp/ccV2ON3C.s 2025-09-09T00:48:28,828 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:28,991 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:28,991 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:28,991 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gromos96format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/gromos96format.' 2025-09-09T00:48:28,993 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/gulpformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/gulpformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:28,996 Using built-in specs. 2025-09-09T00:48:28,997 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:28,997 Target: arm-linux-gnueabihf 2025-09-09T00:48:28,997 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:28,998 Thread model: posix 2025-09-09T00:48:28,998 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:28,998 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:28,998 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gulpformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:28,998 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/gulpformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase gulpformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccbJ9iSp.s 2025-09-09T00:48:29,007 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:29,008 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:29,008 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:29,008 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:29,008 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:29,008 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:29,008 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:29,008 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:29,009 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:29,009 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:29,009 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:29,009 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:29,009 #include "..." search starts here: 2025-09-09T00:48:29,009 #include <...> search starts here: 2025-09-09T00:48:29,009 /usr/include/eigen3 2025-09-09T00:48:29,009 include 2025-09-09T00:48:29,009 /usr/include/python3.13 2025-09-09T00:48:29,009 /usr/include/c++/14 2025-09-09T00:48:29,010 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:29,010 /usr/include/c++/14/backward 2025-09-09T00:48:29,010 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:29,010 /usr/local/include 2025-09-09T00:48:29,010 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:29,010 /usr/include 2025-09-09T00:48:29,010 End of search list. 2025-09-09T00:48:29,027 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:30,519 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:30,520 from include/openbabel/mol.h:43, 2025-09-09T00:48:30,520 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:30,520 from ./src/formats/gulpformat.cpp:16: 2025-09-09T00:48:30,520 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:30,520 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:30,520 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:30,520 | ^ 2025-09-09T00:48:30,520 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:30,521 37 | # define UNUSED(x) x 2025-09-09T00:48:30,521 | ^ 2025-09-09T00:48:31,132 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:31,132 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:31,132 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:31,132 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:31,132 | ^ 2025-09-09T00:48:31,132 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:31,132 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:31,132 | ^~~~~~~~ 2025-09-09T00:48:31,135 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:31,136 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:31,136 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:31,136 | ^ 2025-09-09T00:48:31,136 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:31,136 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:31,136 | ^~~~~~~~ 2025-09-09T00:48:31,150 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:31,150 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:31,150 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:31,150 | ^ 2025-09-09T00:48:31,150 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:31,151 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:31,151 | ^~~~~~~~ 2025-09-09T00:48:31,155 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:31,155 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:31,155 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:31,155 | ^ 2025-09-09T00:48:31,155 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:31,156 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:31,156 | ^~~~~~~~ 2025-09-09T00:48:31,293 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:31,294 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:31,294 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:31,294 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:31,294 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:31,294 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:31,294 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:31,294 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:31,294 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:31,295 from include/openbabel/mol.h:35: 2025-09-09T00:48:31,295 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:31,295 131 | struct binary_function 2025-09-09T00:48:31,295 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:31,456 ./src/formats/gulpformat.cpp: In member function ‘virtual int OpenBabel::GULPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:48:31,456 ./src/formats/gulpformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:48:31,456 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:48:31,457 | ~~~~^ 2025-09-09T00:48:31,457 ./src/formats/gulpformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:48:31,457 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:48:31,457 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:48:33,862 ./src/formats/gulpformat.cpp: In member function ‘virtual bool OpenBabel::GULPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:33,862 ./src/formats/gulpformat.cpp:351:14: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:48:33,862 351 | double en_kcal_per_mole = enthalpy_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:48:33,862 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:48:33,863 ./src/formats/gulpformat.cpp:88:12: note: ‘enthalpy_eV’ was declared here 2025-09-09T00:48:33,863 88 | double enthalpy_eV, pv_eV; 2025-09-09T00:48:33,863 | ^~~~~~~~~~~ 2025-09-09T00:48:33,863 ./src/formats/gulpformat.cpp:352:14: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:48:33,863 352 | double pv_kcal_per_mole = pv_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:48:33,863 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:48:33,863 ./src/formats/gulpformat.cpp:88:25: note: ‘pv_eV’ was declared here 2025-09-09T00:48:33,863 88 | double enthalpy_eV, pv_eV; 2025-09-09T00:48:33,863 | ^~~~~ 2025-09-09T00:48:35,202 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gulpformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:35,202 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/gulpformat.o /tmp/ccbJ9iSp.s 2025-09-09T00:48:35,207 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:35,513 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:35,514 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:35,514 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/gulpformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/gulpformat.' 2025-09-09T00:48:35,515 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/hinformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/hinformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:35,519 Using built-in specs. 2025-09-09T00:48:35,520 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:35,520 Target: arm-linux-gnueabihf 2025-09-09T00:48:35,520 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:35,520 Thread model: posix 2025-09-09T00:48:35,520 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:35,521 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:35,521 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/hinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:35,521 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/hinformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase hinformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccRIMz4B.s 2025-09-09T00:48:35,530 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:35,530 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:35,530 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:35,530 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:35,531 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:35,531 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:35,531 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:35,531 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:35,531 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:35,531 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:35,531 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:35,531 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:35,531 #include "..." search starts here: 2025-09-09T00:48:35,531 #include <...> search starts here: 2025-09-09T00:48:35,532 /usr/include/eigen3 2025-09-09T00:48:35,532 include 2025-09-09T00:48:35,532 /usr/include/python3.13 2025-09-09T00:48:35,532 /usr/include/c++/14 2025-09-09T00:48:35,532 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:35,532 /usr/include/c++/14/backward 2025-09-09T00:48:35,532 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:35,532 /usr/local/include 2025-09-09T00:48:35,532 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:35,532 /usr/include 2025-09-09T00:48:35,532 End of search list. 2025-09-09T00:48:35,546 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:37,057 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:37,057 from include/openbabel/mol.h:43, 2025-09-09T00:48:37,057 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:37,057 from ./src/formats/hinformat.cpp:17: 2025-09-09T00:48:37,058 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:37,058 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:37,058 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:37,058 | ^ 2025-09-09T00:48:37,058 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:37,058 37 | # define UNUSED(x) x 2025-09-09T00:48:37,058 | ^ 2025-09-09T00:48:37,670 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:37,671 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:37,671 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:37,671 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:37,671 | ^ 2025-09-09T00:48:37,671 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:37,671 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:37,671 | ^~~~~~~~ 2025-09-09T00:48:37,674 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:37,675 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:37,675 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:37,675 | ^ 2025-09-09T00:48:37,675 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:37,675 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:37,675 | ^~~~~~~~ 2025-09-09T00:48:37,689 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:37,689 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:37,689 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:37,689 | ^ 2025-09-09T00:48:37,689 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:37,689 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:37,690 | ^~~~~~~~ 2025-09-09T00:48:37,694 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:37,694 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:37,694 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:37,694 | ^ 2025-09-09T00:48:37,694 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:37,695 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:37,695 | ^~~~~~~~ 2025-09-09T00:48:37,832 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:37,833 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:37,833 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:37,833 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:37,833 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:37,833 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:37,833 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:37,833 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:37,833 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:37,833 from include/openbabel/mol.h:35: 2025-09-09T00:48:37,834 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:37,834 131 | struct binary_function 2025-09-09T00:48:37,834 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:40,221 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/hinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:40,221 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/hinformat.o /tmp/ccRIMz4B.s 2025-09-09T00:48:40,227 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:40,414 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:40,414 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:40,414 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/hinformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/hinformat.' 2025-09-09T00:48:40,415 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/jaguarformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/jaguarformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:40,420 Using built-in specs. 2025-09-09T00:48:40,422 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:40,422 Target: arm-linux-gnueabihf 2025-09-09T00:48:40,422 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:40,423 Thread model: posix 2025-09-09T00:48:40,423 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:40,423 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:40,423 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/jaguarformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:40,425 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/jaguarformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase jaguarformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc1bXH0t.s 2025-09-09T00:48:40,437 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:40,437 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:40,437 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:40,437 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:40,437 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:40,437 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:40,438 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:40,438 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:40,438 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:40,438 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:40,438 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:40,438 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:40,438 #include "..." search starts here: 2025-09-09T00:48:40,438 #include <...> search starts here: 2025-09-09T00:48:40,438 /usr/include/eigen3 2025-09-09T00:48:40,439 include 2025-09-09T00:48:40,439 /usr/include/python3.13 2025-09-09T00:48:40,439 /usr/include/c++/14 2025-09-09T00:48:40,439 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:40,439 /usr/include/c++/14/backward 2025-09-09T00:48:40,439 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:40,439 /usr/local/include 2025-09-09T00:48:40,439 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:40,439 /usr/include 2025-09-09T00:48:40,440 End of search list. 2025-09-09T00:48:40,456 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:41,962 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:41,962 from include/openbabel/mol.h:43, 2025-09-09T00:48:41,963 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:41,963 from ./src/formats/jaguarformat.cpp:17: 2025-09-09T00:48:41,963 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:41,963 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:41,963 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:41,963 | ^ 2025-09-09T00:48:41,963 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:41,963 37 | # define UNUSED(x) x 2025-09-09T00:48:41,963 | ^ 2025-09-09T00:48:42,574 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:42,574 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,574 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,574 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:42,574 | ^ 2025-09-09T00:48:42,575 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:42,575 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:42,575 | ^~~~~~~~ 2025-09-09T00:48:42,578 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,578 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,578 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:42,578 | ^ 2025-09-09T00:48:42,578 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:42,578 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:42,578 | ^~~~~~~~ 2025-09-09T00:48:42,592 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,592 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,592 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:42,593 | ^ 2025-09-09T00:48:42,593 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:42,593 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:42,593 | ^~~~~~~~ 2025-09-09T00:48:42,597 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,597 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,598 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:42,598 | ^ 2025-09-09T00:48:42,598 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:42,598 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:42,598 | ^~~~~~~~ 2025-09-09T00:48:42,737 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:42,737 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:42,737 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:42,737 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:42,737 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:42,737 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:42,737 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:42,737 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:42,738 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:42,738 from include/openbabel/mol.h:35: 2025-09-09T00:48:42,738 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:42,738 131 | struct binary_function 2025-09-09T00:48:42,738 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:45,727 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/jaguarformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:45,728 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/jaguarformat.o /tmp/cc1bXH0t.s 2025-09-09T00:48:45,732 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:45,987 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:45,987 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:45,987 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/jaguarformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/jaguarformat.' 2025-09-09T00:48:45,987 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/lmpdatformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/lmpdatformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:45,991 Using built-in specs. 2025-09-09T00:48:45,992 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:45,992 Target: arm-linux-gnueabihf 2025-09-09T00:48:45,992 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:45,993 Thread model: posix 2025-09-09T00:48:45,993 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:45,993 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:45,993 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/lmpdatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:45,993 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/lmpdatformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase lmpdatformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccqUmEjE.s 2025-09-09T00:48:46,010 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:46,010 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:46,010 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:46,010 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:46,010 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:46,011 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:46,011 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:46,011 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:46,011 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:46,011 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:46,011 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:46,011 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:46,011 #include "..." search starts here: 2025-09-09T00:48:46,011 #include <...> search starts here: 2025-09-09T00:48:46,012 /usr/include/eigen3 2025-09-09T00:48:46,012 include 2025-09-09T00:48:46,012 /usr/include/python3.13 2025-09-09T00:48:46,012 /usr/include/c++/14 2025-09-09T00:48:46,012 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:46,012 /usr/include/c++/14/backward 2025-09-09T00:48:46,012 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:46,012 /usr/local/include 2025-09-09T00:48:46,013 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:46,013 /usr/include 2025-09-09T00:48:46,013 End of search list. 2025-09-09T00:48:46,023 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:47,540 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:47,540 from include/openbabel/mol.h:43, 2025-09-09T00:48:47,540 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:47,540 from ./src/formats/lmpdatformat.cpp:15: 2025-09-09T00:48:47,540 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:47,540 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:47,540 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:47,540 | ^ 2025-09-09T00:48:47,541 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:47,541 37 | # define UNUSED(x) x 2025-09-09T00:48:47,541 | ^ 2025-09-09T00:48:48,150 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:48,150 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:48,150 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:48,150 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:48,150 | ^ 2025-09-09T00:48:48,150 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:48,150 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:48,150 | ^~~~~~~~ 2025-09-09T00:48:48,160 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:48,160 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:48,160 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:48,160 | ^ 2025-09-09T00:48:48,160 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:48,160 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:48,160 | ^~~~~~~~ 2025-09-09T00:48:48,170 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:48,170 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:48,170 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:48,170 | ^ 2025-09-09T00:48:48,170 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:48,170 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:48,170 | ^~~~~~~~ 2025-09-09T00:48:48,174 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:48,174 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:48,174 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:48,174 | ^ 2025-09-09T00:48:48,174 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:48,175 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:48,175 | ^~~~~~~~ 2025-09-09T00:48:48,319 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:48,319 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:48,319 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:48,320 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:48,320 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:48,320 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:48,320 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:48,320 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:48,320 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:48,320 from include/openbabel/mol.h:35: 2025-09-09T00:48:48,320 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:48,320 131 | struct binary_function 2025-09-09T00:48:48,320 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:48,539 ./src/formats/lmpdatformat.cpp: In member function ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:48,539 ./src/formats/lmpdatformat.cpp:271:20: warning: unused variable ‘length’ [-Wunused-variable] 2025-09-09T00:48:48,539 271 | double length=cmax-cmin; 2025-09-09T00:48:48,539 | ^~~~~~ 2025-09-09T00:48:48,568 ./src/formats/lmpdatformat.cpp:361:25: warning: unused variable ‘atomid’ [-Wunused-variable] 2025-09-09T00:48:48,568 361 | int atomid=5; 2025-09-09T00:48:48,568 | ^~~~~~ 2025-09-09T00:48:48,568 ./src/formats/lmpdatformat.cpp:362:28: warning: unused variable ‘charge’ [-Wunused-variable] 2025-09-09T00:48:48,569 362 | double charge=0.5; 2025-09-09T00:48:48,569 | ^~~~~~ 2025-09-09T00:48:51,282 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:48:51,282 from include/openbabel/mol.h:37: 2025-09-09T00:48:51,282 /usr/include/c++/14/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> >]’: 2025-09-09T00:48:51,282 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-09T00:48:51,282 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:48:51,282 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:51,904 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:48:51,904 /usr/include/c++/14/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> >]’: 2025-09-09T00:48:51,904 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:48:51,904 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:48:51,904 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:51,904 514 | std::tuple(__k), 2025-09-09T00:48:51,904 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:51,904 515 | std::tuple<>()); 2025-09-09T00:48:51,904 | ~~~~~~~~~~~~~~~ 2025-09-09T00:48:53,024 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> >]’, 2025-09-09T00:48:53,024 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:98:21: 2025-09-09T00:48:53,024 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:48:53,024 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:48:53,024 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:53,024 514 | std::tuple(__k), 2025-09-09T00:48:53,024 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:53,025 515 | std::tuple<>()); 2025-09-09T00:48:53,025 | ~~~~~~~~~~~~~~~ 2025-09-09T00:48:53,041 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> >]’, 2025-09-09T00:48:53,041 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:368:28: 2025-09-09T00:48:53,041 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:48:53,041 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:48:53,041 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:53,041 514 | std::tuple(__k), 2025-09-09T00:48:53,042 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:53,042 515 | std::tuple<>()); 2025-09-09T00:48:53,042 | ~~~~~~~~~~~~~~~ 2025-09-09T00:48:55,586 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/lmpdatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:55,587 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/lmpdatformat.o /tmp/ccqUmEjE.s 2025-09-09T00:48:55,592 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:56,198 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:48:56,198 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:48:56,198 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/lmpdatformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/lmpdatformat.' 2025-09-09T00:48:56,201 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/lpmdformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/lpmdformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:56,205 Using built-in specs. 2025-09-09T00:48:56,206 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:56,206 Target: arm-linux-gnueabihf 2025-09-09T00:48:56,206 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:48:56,206 Thread model: posix 2025-09-09T00:48:56,206 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:56,206 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:56,207 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/lpmdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:48:56,207 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/lpmdformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase lpmdformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccCZDzK1.s 2025-09-09T00:48:56,216 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:56,217 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:48:56,217 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:56,217 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:56,217 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:56,217 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:56,217 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:56,217 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:56,218 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:56,218 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:56,218 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:56,218 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:56,218 #include "..." search starts here: 2025-09-09T00:48:56,218 #include <...> search starts here: 2025-09-09T00:48:56,218 /usr/include/eigen3 2025-09-09T00:48:56,218 include 2025-09-09T00:48:56,218 /usr/include/python3.13 2025-09-09T00:48:56,218 /usr/include/c++/14 2025-09-09T00:48:56,218 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:56,219 /usr/include/c++/14/backward 2025-09-09T00:48:56,219 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:56,219 /usr/local/include 2025-09-09T00:48:56,219 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:56,219 /usr/include 2025-09-09T00:48:56,219 End of search list. 2025-09-09T00:48:56,236 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:57,755 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:57,755 from include/openbabel/mol.h:43, 2025-09-09T00:48:57,755 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:57,756 from ./src/formats/lpmdformat.cpp:15: 2025-09-09T00:48:57,756 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:57,756 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:57,756 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:57,756 | ^ 2025-09-09T00:48:57,756 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:57,756 37 | # define UNUSED(x) x 2025-09-09T00:48:57,756 | ^ 2025-09-09T00:48:58,368 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:58,368 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,368 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,368 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:58,369 | ^ 2025-09-09T00:48:58,369 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:58,369 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:58,369 | ^~~~~~~~ 2025-09-09T00:48:58,372 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,372 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,373 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:58,373 | ^ 2025-09-09T00:48:58,373 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:58,373 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:58,373 | ^~~~~~~~ 2025-09-09T00:48:58,388 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,388 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,388 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:58,388 | ^ 2025-09-09T00:48:58,389 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:58,389 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:58,389 | ^~~~~~~~ 2025-09-09T00:48:58,393 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,393 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,393 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:58,393 | ^ 2025-09-09T00:48:58,394 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:58,394 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:58,394 | ^~~~~~~~ 2025-09-09T00:48:58,536 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:58,536 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:58,537 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:58,537 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:58,537 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:58,537 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:58,537 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:58,537 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:58,537 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:58,537 from include/openbabel/mol.h:35: 2025-09-09T00:48:58,537 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:58,537 131 | struct binary_function 2025-09-09T00:48:58,538 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:58,713 ./src/formats/lpmdformat.cpp: In member function ‘virtual int OpenBabel::LpmdFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:48:58,713 ./src/formats/lpmdformat.cpp:56:31: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:48:58,713 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:48:58,713 | ~~~~^ 2025-09-09T00:48:58,713 ./src/formats/lpmdformat.cpp:56:48: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:48:58,713 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:48:58,713 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:48:58,717 ./src/formats/lpmdformat.cpp: In member function ‘bool OpenBabel::LpmdFormat::ReadHeader(std::istream&, OpenBabel::OBMol&)’: 2025-09-09T00:48:58,718 ./src/formats/lpmdformat.cpp:91:56: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:48:58,718 91 | bool LpmdFormat::ReadHeader( std::istream &ifs, OBMol &mol ) 2025-09-09T00:48:58,718 | ~~~~~~~^~~ 2025-09-09T00:48:58,722 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:58,722 ./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] 2025-09-09T00:48:58,723 190 | if(int(headers.size()-1)!=tokens.size()) 2025-09-09T00:48:58,723 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2025-09-09T00:48:58,725 ./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] 2025-09-09T00:48:58,726 204 | for(int i=1 ; i < headers.size() ; ++i) //the first element is HDR 2025-09-09T00:48:58,726 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:48:58,731 ./src/formats/lpmdformat.cpp:237:11: warning: unused variable ‘FX’ [-Wunused-variable] 2025-09-09T00:48:58,731 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2025-09-09T00:48:58,731 | ^~ 2025-09-09T00:48:58,731 ./src/formats/lpmdformat.cpp:237:32: warning: unused variable ‘FY’ [-Wunused-variable] 2025-09-09T00:48:58,731 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2025-09-09T00:48:58,732 | ^~ 2025-09-09T00:48:58,732 ./src/formats/lpmdformat.cpp:237:53: warning: unused variable ‘FZ’ [-Wunused-variable] 2025-09-09T00:48:58,732 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2025-09-09T00:48:58,732 | ^~ 2025-09-09T00:48:58,747 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:58,747 ./src/formats/lpmdformat.cpp:360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:48:58,747 360 | for(int i=0; i < mol.NumAtoms() ; ++i) 2025-09-09T00:48:58,747 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:48:58,749 ./src/formats/lpmdformat.cpp:376:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:48:58,749 376 | for(int i=0;iGetAtomicNum()), 2025-09-09T00:49:05,359 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:05,359 381 | tmp.GetX(), 2025-09-09T00:49:05,359 | ~~~~~~~~~~~ 2025-09-09T00:49:05,359 382 | tmp.GetY(), 2025-09-09T00:49:05,359 | ~~~~~~~~~~~ 2025-09-09T00:49:05,359 383 | tmp.GetZ()); 2025-09-09T00:49:05,359 | ~~~~~~~~~~~ 2025-09-09T00:49:05,360 ./src/formats/lpmdformat.cpp:388:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:49:05,360 388 | snprintf(buffer, BUFF_SIZE, "%15.5f%15.5f%15.5f",v.x(),v.y(),v.z()); 2025-09-09T00:49:05,360 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:05,360 ./src/formats/lpmdformat.cpp:401:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:49:05,360 401 | snprintf(buffer, BUFF_SIZE, "%15.5f%15.5f%15.5f",force.x(),force.y(),force.z()); 2025-09-09T00:49:05,360 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:05,360 ./src/formats/lpmdformat.cpp:395:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:49:05,360 395 | snprintf(buffer, BUFF_SIZE, "%15.5f%15.5f%15.5f",a.x(),a.y(),a.z()); 2025-09-09T00:49:05,360 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:05,360 ./src/formats/lpmdformat.cpp:406:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:49:05,361 406 | snprintf(buffer, BUFF_SIZE, "%15.5f", atom -> GetPartialCharge()); 2025-09-09T00:49:05,361 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:07,412 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/lpmdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:07,412 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/lpmdformat.o /tmp/ccCZDzK1.s 2025-09-09T00:49:07,417 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:08,149 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:49:08,149 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:49:08,149 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/lpmdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/lpmdformat.' 2025-09-09T00:49:08,152 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mdffformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mdffformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:49:08,156 Using built-in specs. 2025-09-09T00:49:08,157 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:08,157 Target: arm-linux-gnueabihf 2025-09-09T00:49:08,157 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:49:08,157 Thread model: posix 2025-09-09T00:49:08,157 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:08,157 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:08,157 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mdffformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:08,157 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mdffformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mdffformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccYRqROL.s 2025-09-09T00:49:08,167 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:08,167 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:49:08,167 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:08,167 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:08,167 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:08,167 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:08,168 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:08,168 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:08,168 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:08,168 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:08,168 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:08,168 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:08,168 #include "..." search starts here: 2025-09-09T00:49:08,168 #include <...> search starts here: 2025-09-09T00:49:08,168 /usr/include/eigen3 2025-09-09T00:49:08,168 include 2025-09-09T00:49:08,169 /usr/include/python3.13 2025-09-09T00:49:08,169 /usr/include/c++/14 2025-09-09T00:49:08,169 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:08,169 /usr/include/c++/14/backward 2025-09-09T00:49:08,169 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:08,169 /usr/local/include 2025-09-09T00:49:08,169 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:08,169 /usr/include 2025-09-09T00:49:08,169 End of search list. 2025-09-09T00:49:08,184 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:09,684 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:09,684 from include/openbabel/mol.h:43, 2025-09-09T00:49:09,685 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:09,685 from ./src/formats/mdffformat.cpp:17: 2025-09-09T00:49:09,685 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:09,685 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:09,685 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:09,685 | ^ 2025-09-09T00:49:09,685 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:09,685 37 | # define UNUSED(x) x 2025-09-09T00:49:09,685 | ^ 2025-09-09T00:49:10,295 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:10,295 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:10,295 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:10,295 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:10,296 | ^ 2025-09-09T00:49:10,296 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:10,296 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:10,296 | ^~~~~~~~ 2025-09-09T00:49:10,299 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:10,299 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:10,299 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:10,299 | ^ 2025-09-09T00:49:10,299 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:10,300 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:10,300 | ^~~~~~~~ 2025-09-09T00:49:10,313 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:10,314 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:10,314 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:10,314 | ^ 2025-09-09T00:49:10,314 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:10,314 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:10,314 | ^~~~~~~~ 2025-09-09T00:49:10,318 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:10,318 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:10,319 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:10,319 | ^ 2025-09-09T00:49:10,319 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:10,319 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:10,319 | ^~~~~~~~ 2025-09-09T00:49:10,460 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:10,460 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:10,460 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:10,460 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:10,460 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:10,460 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:10,461 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:10,461 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:10,461 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:10,461 from include/openbabel/mol.h:35: 2025-09-09T00:49:10,461 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:10,461 131 | struct binary_function 2025-09-09T00:49:10,461 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:10,753 ./src/formats/mdffformat.cpp: In member function ‘virtual int OpenBabel::MDFFFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:49:10,753 ./src/formats/mdffformat.cpp:71:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:49:10,753 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:49:10,753 | ~~~~^ 2025-09-09T00:49:10,753 ./src/formats/mdffformat.cpp:71:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:10,754 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:49:10,754 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:10,779 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:10,779 ./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] 2025-09-09T00:49:10,779 241 | for(int i = 0; i < atom_t_prop.size(); i++) 2025-09-09T00:49:10,779 | ~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:10,781 ./src/formats/mdffformat.cpp:262:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:49:10,781 262 | for(unsigned int j = 0; j < atom_t_prop[i].num_of_atoms; j++) 2025-09-09T00:49:10,781 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:10,789 ./src/formats/mdffformat.cpp: In member function ‘bool OpenBabel::aindx::operator<(const OpenBabel::aindx&) const’: 2025-09-09T00:49:10,789 ./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] 2025-09-09T00:49:10,789 321 | for(int i = 0; i < vs.size(); i++) 2025-09-09T00:49:10,789 | ~~^~~~~~~~~~~ 2025-09-09T00:49:10,818 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:10,818 ./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] 2025-09-09T00:49:10,818 380 | for(int i = 0; i < vs.size(); i++) 2025-09-09T00:49:10,818 | ~~^~~~~~~~~~~ 2025-09-09T00:49:10,875 ./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] 2025-09-09T00:49:10,875 435 | for (int i = 0; i < atypes_def.size(); i++) 2025-09-09T00:49:10,875 | ~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:10,876 ./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] 2025-09-09T00:49:10,876 442 | for (int i = 0; i < atypes_def.size(); i++) 2025-09-09T00:49:10,876 | ~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:10,908 ./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] 2025-09-09T00:49:10,908 492 | for(int j = 0; j < atypes_def.size(); j++) 2025-09-09T00:49:10,908 | ~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:14,123 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:49:14,123 from include/openbabel/mol.h:37: 2025-09-09T00:49:14,123 /usr/include/c++/14/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> >]’: 2025-09-09T00:49:14,123 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-09T00:49:14,123 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:49:14,123 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,164 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:49:18,164 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> >]’, 2025-09-09T00:49:18,165 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:464:23: 2025-09-09T00:49:18,165 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:49:18,165 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:49:18,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,165 514 | std::tuple(__k), 2025-09-09T00:49:18,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,165 515 | std::tuple<>()); 2025-09-09T00:49:18,165 | ~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,165 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> >]’, 2025-09-09T00:49:18,166 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:466:26: 2025-09-09T00:49:18,166 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:49:18,166 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:49:18,166 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,166 514 | std::tuple(__k), 2025-09-09T00:49:18,166 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,166 515 | std::tuple<>()); 2025-09-09T00:49:18,166 | ~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,166 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> >]’, 2025-09-09T00:49:18,167 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:467:25: 2025-09-09T00:49:18,167 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:49:18,167 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:49:18,167 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,167 514 | std::tuple(__k), 2025-09-09T00:49:18,167 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,167 515 | std::tuple<>()); 2025-09-09T00:49:18,167 | ~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,171 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> >]’, 2025-09-09T00:49:18,171 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:499:53: 2025-09-09T00:49:18,171 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:49:18,171 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:49:18,172 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,172 514 | std::tuple(__k), 2025-09-09T00:49:18,172 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:18,172 515 | std::tuple<>()); 2025-09-09T00:49:18,172 | ~~~~~~~~~~~~~~~ 2025-09-09T00:49:20,136 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mdffformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:20,137 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mdffformat.o /tmp/ccYRqROL.s 2025-09-09T00:49:20,145 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:20,918 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:49:20,918 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:49:20,918 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mdffformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mdffformat.' 2025-09-09T00:49:20,921 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mdlformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mdlformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:49:20,926 Using built-in specs. 2025-09-09T00:49:20,926 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:20,927 Target: arm-linux-gnueabihf 2025-09-09T00:49:20,927 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:49:20,927 Thread model: posix 2025-09-09T00:49:20,927 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:20,927 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:20,927 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mdlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:20,927 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mdlformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mdlformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc1lzef2.s 2025-09-09T00:49:20,938 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:20,938 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:49:20,939 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:20,939 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:20,940 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:20,940 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:20,940 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:20,940 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:20,940 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:20,940 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:20,940 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:20,941 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:20,941 #include "..." search starts here: 2025-09-09T00:49:20,941 #include <...> search starts here: 2025-09-09T00:49:20,941 /usr/include/eigen3 2025-09-09T00:49:20,941 include 2025-09-09T00:49:20,941 /usr/include/python3.13 2025-09-09T00:49:20,941 /usr/include/c++/14 2025-09-09T00:49:20,942 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:20,942 /usr/include/c++/14/backward 2025-09-09T00:49:20,942 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:20,942 /usr/local/include 2025-09-09T00:49:20,942 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:20,942 /usr/include 2025-09-09T00:49:20,942 End of search list. 2025-09-09T00:49:20,961 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:22,690 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:22,691 from include/openbabel/mol.h:43, 2025-09-09T00:49:22,691 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:22,691 from ./src/formats/mdlformat.cpp:26: 2025-09-09T00:49:22,691 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:22,691 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:22,691 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:22,691 | ^ 2025-09-09T00:49:22,691 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:22,691 37 | # define UNUSED(x) x 2025-09-09T00:49:22,692 | ^ 2025-09-09T00:49:23,246 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:23,246 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:23,246 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:23,246 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:23,246 | ^ 2025-09-09T00:49:23,246 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:23,247 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:23,247 | ^~~~~~~~ 2025-09-09T00:49:23,250 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:23,250 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:23,250 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:23,250 | ^ 2025-09-09T00:49:23,250 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:23,250 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:23,250 | ^~~~~~~~ 2025-09-09T00:49:23,264 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:23,264 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:23,264 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:23,265 | ^ 2025-09-09T00:49:23,265 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:23,265 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:23,265 | ^~~~~~~~ 2025-09-09T00:49:23,269 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:23,269 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:23,269 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:23,269 | ^ 2025-09-09T00:49:23,270 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:23,270 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:23,270 | ^~~~~~~~ 2025-09-09T00:49:23,414 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:23,414 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:23,414 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:23,414 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:23,414 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:23,414 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:23,415 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:23,415 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:23,415 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:23,415 from ./src/formats/mdlformat.cpp:22: 2025-09-09T00:49:23,415 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:23,415 131 | struct binary_function 2025-09-09T00:49:23,415 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:23,908 In file included from ./src/formats/mdlformat.cpp:34: 2025-09-09T00:49:23,908 include/formats/mdlvalence.h: In function ‘unsigned int MDLValence(unsigned int, int, unsigned int)’: 2025-09-09T00:49:23,908 include/formats/mdlvalence.h:51:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,908 51 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,908 | ^~ 2025-09-09T00:49:23,909 include/formats/mdlvalence.h:51:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,909 51 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,909 | ^~~~~ 2025-09-09T00:49:23,909 include/formats/mdlvalence.h:64:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,909 64 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,909 | ^~ 2025-09-09T00:49:23,909 include/formats/mdlvalence.h:64:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,909 64 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,909 | ^~~~~ 2025-09-09T00:49:23,910 include/formats/mdlvalence.h:77:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,910 77 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,910 | ^~ 2025-09-09T00:49:23,910 include/formats/mdlvalence.h:77:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,910 77 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,910 | ^~~~~ 2025-09-09T00:49:23,910 include/formats/mdlvalence.h:90:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,910 90 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,910 | ^~ 2025-09-09T00:49:23,910 include/formats/mdlvalence.h:90:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,911 90 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,911 | ^~~~~ 2025-09-09T00:49:23,911 include/formats/mdlvalence.h:103:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,911 103 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,911 | ^~ 2025-09-09T00:49:23,911 include/formats/mdlvalence.h:103:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,911 103 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,911 | ^~~~~ 2025-09-09T00:49:23,911 include/formats/mdlvalence.h:116:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,911 116 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,912 | ^~ 2025-09-09T00:49:23,912 include/formats/mdlvalence.h:116:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,912 116 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,912 | ^~~~~ 2025-09-09T00:49:23,912 include/formats/mdlvalence.h:119:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,912 119 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,912 | ^~ 2025-09-09T00:49:23,912 include/formats/mdlvalence.h:119:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,912 119 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,912 | ^~~~~ 2025-09-09T00:49:23,912 include/formats/mdlvalence.h:121:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,913 121 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,913 | ^~ 2025-09-09T00:49:23,913 include/formats/mdlvalence.h:121:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,913 121 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,913 | ^~~~~ 2025-09-09T00:49:23,913 include/formats/mdlvalence.h:134:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,913 134 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,913 | ^~ 2025-09-09T00:49:23,913 include/formats/mdlvalence.h:134:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,913 134 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,914 | ^~~~~ 2025-09-09T00:49:23,914 include/formats/mdlvalence.h:137:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,914 137 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,914 | ^~ 2025-09-09T00:49:23,914 include/formats/mdlvalence.h:137:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,914 137 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,914 | ^~~~~ 2025-09-09T00:49:23,914 include/formats/mdlvalence.h:139:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,914 139 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,914 | ^~ 2025-09-09T00:49:23,915 include/formats/mdlvalence.h:139:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,915 139 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,915 | ^~~~~ 2025-09-09T00:49:23,915 include/formats/mdlvalence.h:152:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,915 152 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,915 | ^~ 2025-09-09T00:49:23,915 include/formats/mdlvalence.h:152:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,915 152 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,915 | ^~~~~ 2025-09-09T00:49:23,915 include/formats/mdlvalence.h:155:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,915 155 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,916 | ^~ 2025-09-09T00:49:23,916 include/formats/mdlvalence.h:155:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,916 155 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,916 | ^~~~~ 2025-09-09T00:49:23,916 include/formats/mdlvalence.h:157:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,916 157 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,916 | ^~ 2025-09-09T00:49:23,916 include/formats/mdlvalence.h:157:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,916 157 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,916 | ^~~~~ 2025-09-09T00:49:23,916 include/formats/mdlvalence.h:170:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,917 170 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,917 | ^~ 2025-09-09T00:49:23,917 include/formats/mdlvalence.h:170:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,917 170 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,917 | ^~~~~ 2025-09-09T00:49:23,917 include/formats/mdlvalence.h:173:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,917 173 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,917 | ^~ 2025-09-09T00:49:23,917 include/formats/mdlvalence.h:173:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,917 173 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,918 | ^~~~~ 2025-09-09T00:49:23,918 include/formats/mdlvalence.h:175:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,918 175 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,918 | ^~ 2025-09-09T00:49:23,918 include/formats/mdlvalence.h:175:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,918 175 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,918 | ^~~~~ 2025-09-09T00:49:23,918 include/formats/mdlvalence.h:188:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,918 188 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,918 | ^~ 2025-09-09T00:49:23,919 include/formats/mdlvalence.h:188:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,919 188 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,919 | ^~~~~ 2025-09-09T00:49:23,919 include/formats/mdlvalence.h:191:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,919 191 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,919 | ^~ 2025-09-09T00:49:23,919 include/formats/mdlvalence.h:191:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,919 191 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,919 | ^~~~~ 2025-09-09T00:49:23,919 include/formats/mdlvalence.h:193:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,919 193 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,920 | ^~ 2025-09-09T00:49:23,920 include/formats/mdlvalence.h:193:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,920 193 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,920 | ^~~~~ 2025-09-09T00:49:23,920 include/formats/mdlvalence.h:206:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,920 206 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,920 | ^~ 2025-09-09T00:49:23,920 include/formats/mdlvalence.h:206:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,920 206 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,920 | ^~~~~ 2025-09-09T00:49:23,921 include/formats/mdlvalence.h:209:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,921 209 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,921 | ^~ 2025-09-09T00:49:23,921 include/formats/mdlvalence.h:209:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,921 209 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,921 | ^~~~~ 2025-09-09T00:49:23,921 include/formats/mdlvalence.h:211:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,921 211 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,921 | ^~ 2025-09-09T00:49:23,921 include/formats/mdlvalence.h:211:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,921 211 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,922 | ^~~~~ 2025-09-09T00:49:23,922 include/formats/mdlvalence.h:223:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,922 223 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,922 | ^~ 2025-09-09T00:49:23,922 include/formats/mdlvalence.h:223:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,922 223 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,922 | ^~~~~ 2025-09-09T00:49:23,922 include/formats/mdlvalence.h:226:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,922 226 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,922 | ^~ 2025-09-09T00:49:23,922 include/formats/mdlvalence.h:226:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,923 226 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,923 | ^~~~~ 2025-09-09T00:49:23,923 include/formats/mdlvalence.h:228:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,923 228 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,923 | ^~ 2025-09-09T00:49:23,923 include/formats/mdlvalence.h:228:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,923 228 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,923 | ^~~~~ 2025-09-09T00:49:23,923 include/formats/mdlvalence.h:240:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,923 240 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,924 | ^~ 2025-09-09T00:49:23,924 include/formats/mdlvalence.h:240:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,924 240 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,924 | ^~~~~ 2025-09-09T00:49:23,924 include/formats/mdlvalence.h:243:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,924 243 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,924 | ^~ 2025-09-09T00:49:23,924 include/formats/mdlvalence.h:243:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,924 243 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,924 | ^~~~~ 2025-09-09T00:49:23,924 include/formats/mdlvalence.h:245:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,925 245 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,925 | ^~ 2025-09-09T00:49:23,925 include/formats/mdlvalence.h:245:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,925 245 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,925 | ^~~~~ 2025-09-09T00:49:23,925 include/formats/mdlvalence.h:257:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,925 257 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,925 | ^~ 2025-09-09T00:49:23,925 include/formats/mdlvalence.h:257:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,925 257 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,925 | ^~~~~ 2025-09-09T00:49:23,926 include/formats/mdlvalence.h:260:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,926 260 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,926 | ^~ 2025-09-09T00:49:23,926 include/formats/mdlvalence.h:260:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,926 260 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,926 | ^~~~~ 2025-09-09T00:49:23,926 include/formats/mdlvalence.h:262:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,926 262 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,926 | ^~ 2025-09-09T00:49:23,926 include/formats/mdlvalence.h:262:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,926 262 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,927 | ^~~~~ 2025-09-09T00:49:23,927 include/formats/mdlvalence.h:274:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,927 274 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,927 | ^~ 2025-09-09T00:49:23,927 include/formats/mdlvalence.h:274:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,927 274 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,927 | ^~~~~ 2025-09-09T00:49:23,927 include/formats/mdlvalence.h:277:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,927 277 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,927 | ^~ 2025-09-09T00:49:23,927 include/formats/mdlvalence.h:277:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,928 277 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,928 | ^~~~~ 2025-09-09T00:49:23,928 include/formats/mdlvalence.h:279:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,928 279 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,928 | ^~ 2025-09-09T00:49:23,928 include/formats/mdlvalence.h:279:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,928 279 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,928 | ^~~~~ 2025-09-09T00:49:23,928 include/formats/mdlvalence.h:291:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,928 291 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,929 | ^~ 2025-09-09T00:49:23,929 include/formats/mdlvalence.h:291:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,929 291 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,929 | ^~~~~ 2025-09-09T00:49:23,929 include/formats/mdlvalence.h:294:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,929 294 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,929 | ^~ 2025-09-09T00:49:23,929 include/formats/mdlvalence.h:294:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,929 294 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,930 | ^~~~~ 2025-09-09T00:49:23,930 include/formats/mdlvalence.h:296:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,930 296 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,930 | ^~ 2025-09-09T00:49:23,930 include/formats/mdlvalence.h:296:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,930 296 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,930 | ^~~~~ 2025-09-09T00:49:23,930 include/formats/mdlvalence.h:298:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,930 298 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,931 | ^~ 2025-09-09T00:49:23,931 include/formats/mdlvalence.h:298:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,931 298 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,931 | ^~~~~ 2025-09-09T00:49:23,931 include/formats/mdlvalence.h:310:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,931 310 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,931 | ^~ 2025-09-09T00:49:23,931 include/formats/mdlvalence.h:310:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,931 310 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,931 | ^~~~~ 2025-09-09T00:49:23,931 include/formats/mdlvalence.h:313:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,932 313 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,932 | ^~ 2025-09-09T00:49:23,932 include/formats/mdlvalence.h:313:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,932 313 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,932 | ^~~~~ 2025-09-09T00:49:23,932 include/formats/mdlvalence.h:315:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,932 315 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,932 | ^~ 2025-09-09T00:49:23,932 include/formats/mdlvalence.h:315:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,932 315 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,933 | ^~~~~ 2025-09-09T00:49:23,933 include/formats/mdlvalence.h:317:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,933 317 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,933 | ^~ 2025-09-09T00:49:23,933 include/formats/mdlvalence.h:317:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,933 317 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,933 | ^~~~~ 2025-09-09T00:49:23,933 include/formats/mdlvalence.h:329:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,933 329 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,933 | ^~ 2025-09-09T00:49:23,934 include/formats/mdlvalence.h:329:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,934 329 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,934 | ^~~~~ 2025-09-09T00:49:23,934 include/formats/mdlvalence.h:332:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,934 332 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,934 | ^~ 2025-09-09T00:49:23,934 include/formats/mdlvalence.h:332:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,934 332 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,934 | ^~~~~ 2025-09-09T00:49:23,935 include/formats/mdlvalence.h:334:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,935 334 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,935 | ^~ 2025-09-09T00:49:23,935 include/formats/mdlvalence.h:334:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,935 334 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,935 | ^~~~~ 2025-09-09T00:49:23,935 include/formats/mdlvalence.h:336:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,935 336 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,935 | ^~ 2025-09-09T00:49:23,935 include/formats/mdlvalence.h:336:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,936 336 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,936 | ^~~~~ 2025-09-09T00:49:23,936 include/formats/mdlvalence.h:348:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,936 348 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,936 | ^~ 2025-09-09T00:49:23,936 include/formats/mdlvalence.h:348:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,936 348 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,936 | ^~~~~ 2025-09-09T00:49:23,936 include/formats/mdlvalence.h:351:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,936 351 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,936 | ^~ 2025-09-09T00:49:23,937 include/formats/mdlvalence.h:351:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,937 351 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,937 | ^~~~~ 2025-09-09T00:49:23,937 include/formats/mdlvalence.h:353:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,937 353 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,937 | ^~ 2025-09-09T00:49:23,937 include/formats/mdlvalence.h:353:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,937 353 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,937 | ^~~~~ 2025-09-09T00:49:23,938 include/formats/mdlvalence.h:355:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,938 355 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,938 | ^~ 2025-09-09T00:49:23,938 include/formats/mdlvalence.h:355:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,938 355 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,938 | ^~~~~ 2025-09-09T00:49:23,938 include/formats/mdlvalence.h:367:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,938 367 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,938 | ^~ 2025-09-09T00:49:23,938 include/formats/mdlvalence.h:367:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,939 367 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,939 | ^~~~~ 2025-09-09T00:49:23,939 include/formats/mdlvalence.h:370:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,939 370 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,939 | ^~ 2025-09-09T00:49:23,939 include/formats/mdlvalence.h:370:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,939 370 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,939 | ^~~~~ 2025-09-09T00:49:23,939 include/formats/mdlvalence.h:372:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,940 372 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,940 | ^~ 2025-09-09T00:49:23,940 include/formats/mdlvalence.h:372:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,940 372 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,940 | ^~~~~ 2025-09-09T00:49:23,940 include/formats/mdlvalence.h:374:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,940 374 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,940 | ^~ 2025-09-09T00:49:23,940 include/formats/mdlvalence.h:374:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,941 374 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,941 | ^~~~~ 2025-09-09T00:49:23,941 include/formats/mdlvalence.h:385:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,941 385 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,941 | ^~ 2025-09-09T00:49:23,941 include/formats/mdlvalence.h:385:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,941 385 | if (val <= 7) return 7; break; 2025-09-09T00:49:23,941 | ^~~~~ 2025-09-09T00:49:23,941 include/formats/mdlvalence.h:388:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,941 388 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,942 | ^~ 2025-09-09T00:49:23,942 include/formats/mdlvalence.h:388:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,942 388 | if (val <= 6) return 6; break; 2025-09-09T00:49:23,942 | ^~~~~ 2025-09-09T00:49:23,942 include/formats/mdlvalence.h:390:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,942 390 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,942 | ^~ 2025-09-09T00:49:23,942 include/formats/mdlvalence.h:390:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,942 390 | if (val <= 5) return 5; break; 2025-09-09T00:49:23,942 | ^~~~~ 2025-09-09T00:49:23,943 include/formats/mdlvalence.h:392:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,943 392 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,943 | ^~ 2025-09-09T00:49:23,943 include/formats/mdlvalence.h:392:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,943 392 | if (val <= 4) return 4; break; 2025-09-09T00:49:23,943 | ^~~~~ 2025-09-09T00:49:23,943 include/formats/mdlvalence.h:394:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:49:23,943 394 | if (val <= 3) return 3; break; 2025-09-09T00:49:23,943 | ^~ 2025-09-09T00:49:23,943 include/formats/mdlvalence.h:394:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:49:23,943 394 | if (val <= 3) return 3; break; 2025-09-09T00:49:23,944 | ^~~~~ 2025-09-09T00:49:23,944 include/formats/mdlvalence.h: In function ‘unsigned int HYDValence(unsigned int, int, unsigned int)’: 2025-09-09T00:49:23,944 include/formats/mdlvalence.h:416:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:49:23,944 416 | if (val > impval) { 2025-09-09T00:49:23,944 | ~~~~^~~~~~~~ 2025-09-09T00:49:24,270 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadV3000Block(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, bool)’: 2025-09-09T00:49:24,270 ./src/formats/mdlformat.cpp:1273:85: warning: unused parameter ‘DoMany’ [-Wunused-parameter] 2025-09-09T00:49:24,270 1273 | bool MDLFormat::ReadV3000Block(istream& ifs, OBMol& mol, OBConversion* pConv,bool DoMany) 2025-09-09T00:49:24,270 | ~~~~~^~~~~~ 2025-09-09T00:49:24,280 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadAtomBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:49:24,280 ./src/formats/mdlformat.cpp:1341:10: warning: unused variable ‘chiralWatch’ [-Wunused-variable] 2025-09-09T00:49:24,280 1341 | bool chiralWatch=false; 2025-09-09T00:49:24,280 | ^~~~~~~~~~~ 2025-09-09T00:49:24,280 ./src/formats/mdlformat.cpp:1338:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:24,280 1338 | bool MDLFormat::ReadAtomBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:49:24,280 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:24,290 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadBondBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:49:24,290 ./src/formats/mdlformat.cpp:1422:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:24,290 1422 | bool MDLFormat::ReadBondBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:49:24,290 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:24,290 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadUnimplementedBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, std::string&)’: 2025-09-09T00:49:24,290 ./src/formats/mdlformat.cpp:1481:62: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:49:24,290 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2025-09-09T00:49:24,290 | ~~~~~~~^~~ 2025-09-09T00:49:24,291 ./src/formats/mdlformat.cpp:1481:81: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:24,291 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2025-09-09T00:49:24,291 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:24,291 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadRGroupBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:49:24,291 ./src/formats/mdlformat.cpp:1497:55: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:49:24,291 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:49:24,291 | ~~~~~~~^~~ 2025-09-09T00:49:24,291 ./src/formats/mdlformat.cpp:1497:74: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:24,291 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:49:24,292 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:24,306 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::WriteV3000(std::ostream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:49:24,306 ./src/formats/mdlformat.cpp:1514:69: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:24,306 1514 | bool MDLFormat::WriteV3000(ostream& ofs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:49:24,306 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:24,410 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2025-09-09T00:49:24,410 ./src/formats/mdlformat.cpp:1957:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:49:24,410 1957 | unsigned int second = (a1_b2 == NULL) ? OBStereo::ImplicitRef : a1_b2->GetNbrAtom(a1)->GetId(); 2025-09-09T00:49:24,411 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:24,411 ./src/formats/mdlformat.cpp:1958:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:49:24,411 1958 | unsigned int fourth = (a2_b2 == NULL) ? OBStereo::ImplicitRef : a2_b2->GetNbrAtom(a2)->GetId(); 2025-09-09T00:49:24,411 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:26,060 ./src/formats/mdlformat.cpp: In member function ‘virtual bool OpenBabel::MDLFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:26,060 ./src/formats/mdlformat.cpp:527:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:49:26,061 527 | flag |= OBBond::CisOrTrans; 2025-09-09T00:49:26,061 | ~~~~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:26,061 ./src/formats/mdlformat.cpp:528:15: note: here 2025-09-09T00:49:26,061 528 | case 4: 2025-09-09T00:49:26,061 | ^~~~ 2025-09-09T00:49:31,949 ./src/formats/mdlformat.cpp: In member function ‘std::string OpenBabel::MDLFormat::GetTimeDate()’: 2025-09-09T00:49:31,949 ./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=] 2025-09-09T00:49:31,949 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2025-09-09T00:49:31,949 | ^~~~ 2025-09-09T00:49:31,949 ./src/formats/mdlformat.cpp:1648:22: note: directive argument in the range [-2147483648, 2147483547] 2025-09-09T00:49:31,949 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2025-09-09T00:49:31,949 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:31,950 ./src/formats/mdlformat.cpp:1648:13: note: ‘snprintf’ output between 11 and 56 bytes into a destination of size 11 2025-09-09T00:49:31,950 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2025-09-09T00:49:31,950 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:31,950 1649 | ((ts->tm_year>=100)? ts->tm_year-100 : ts->tm_year), 2025-09-09T00:49:31,950 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:31,950 1650 | ts->tm_hour, ts->tm_min); 2025-09-09T00:49:31,950 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:33,251 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2025-09-09T00:49:33,252 ./src/formats/mdlformat.cpp:1961:7: warning: ‘a1_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:49:33,252 1961 | if (a1_stereo == a2_stereo) 2025-09-09T00:49:33,252 | ^~ 2025-09-09T00:49:33,252 ./src/formats/mdlformat.cpp:1926:31: note: ‘a1_stereo’ was declared here 2025-09-09T00:49:33,252 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2025-09-09T00:49:33,252 | ^~~~~~~~~ 2025-09-09T00:49:33,253 ./src/formats/mdlformat.cpp:1961:7: warning: ‘a2_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:49:33,253 1961 | if (a1_stereo == a2_stereo) 2025-09-09T00:49:33,253 | ^~ 2025-09-09T00:49:33,253 ./src/formats/mdlformat.cpp:1926:42: note: ‘a2_stereo’ was declared here 2025-09-09T00:49:33,253 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2025-09-09T00:49:33,253 | ^~~~~~~~~ 2025-09-09T00:49:42,207 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mdlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:42,208 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mdlformat.o /tmp/cc1lzef2.s 2025-09-09T00:49:42,213 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:43,717 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:49:43,718 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:49:43,718 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mdlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mdlformat.' 2025-09-09T00:49:43,723 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mmcifformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mmcifformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:49:43,727 Using built-in specs. 2025-09-09T00:49:43,728 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:43,729 Target: arm-linux-gnueabihf 2025-09-09T00:49:43,729 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:49:43,729 Thread model: posix 2025-09-09T00:49:43,729 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:43,730 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:43,730 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mmcifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:43,732 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mmcifformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mmcifformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccgR22pJ.s 2025-09-09T00:49:43,743 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:43,743 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:49:43,744 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:43,744 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:43,745 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:43,745 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:43,746 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:43,746 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:43,746 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:43,746 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:43,746 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:43,747 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:43,747 #include "..." search starts here: 2025-09-09T00:49:43,747 #include <...> search starts here: 2025-09-09T00:49:43,748 /usr/include/eigen3 2025-09-09T00:49:43,748 include 2025-09-09T00:49:43,748 /usr/include/python3.13 2025-09-09T00:49:43,748 /usr/include/c++/14 2025-09-09T00:49:43,748 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:43,749 /usr/include/c++/14/backward 2025-09-09T00:49:43,749 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:43,749 /usr/local/include 2025-09-09T00:49:43,749 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:43,749 /usr/include 2025-09-09T00:49:43,749 End of search list. 2025-09-09T00:49:43,771 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:45,290 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:45,291 from include/openbabel/mol.h:43, 2025-09-09T00:49:45,291 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:45,291 from ./src/formats/mmcifformat.cpp:19: 2025-09-09T00:49:45,291 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:45,291 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:45,291 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:45,291 | ^ 2025-09-09T00:49:45,291 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:45,291 37 | # define UNUSED(x) x 2025-09-09T00:49:45,291 | ^ 2025-09-09T00:49:45,902 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:45,902 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:45,902 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:45,902 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:45,902 | ^ 2025-09-09T00:49:45,902 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:45,903 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:45,903 | ^~~~~~~~ 2025-09-09T00:49:45,907 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:45,907 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:45,907 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:45,907 | ^ 2025-09-09T00:49:45,907 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:45,907 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:45,907 | ^~~~~~~~ 2025-09-09T00:49:45,922 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:45,922 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:45,922 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:45,922 | ^ 2025-09-09T00:49:45,923 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:45,923 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:45,923 | ^~~~~~~~ 2025-09-09T00:49:45,928 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:45,928 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:45,928 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:45,928 | ^ 2025-09-09T00:49:45,928 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:45,929 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:45,929 | ^~~~~~~~ 2025-09-09T00:49:46,067 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:46,067 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:46,067 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:46,068 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:46,068 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:46,068 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:46,068 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:46,069 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:46,069 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:46,069 from include/openbabel/mol.h:35: 2025-09-09T00:49:46,069 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:46,069 131 | struct binary_function 2025-09-09T00:49:46,069 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:47,702 ./src/formats/mmcifformat.cpp: In member function ‘bool OpenBabel::CIFLexer::next_token(Token&)’: 2025-09-09T00:49:47,703 ./src/formats/mmcifformat.cpp:394:8: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:49:47,703 394 | if (last_char == '\n') 2025-09-09T00:49:47,703 | ^~ 2025-09-09T00:49:47,703 ./src/formats/mmcifformat.cpp:421:6: note: here 2025-09-09T00:49:47,703 421 | default: // reading an un-quoted text string 2025-09-09T00:49:47,703 | ^~~~~~~ 2025-09-09T00:49:47,712 ./src/formats/mmcifformat.cpp: In member function ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:47,712 ./src/formats/mmcifformat.cpp:638:16: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:49:47,712 638 | if(string::npos != token.as_text.find_first_of("0123456789")) 2025-09-09T00:49:47,712 | ^~ 2025-09-09T00:49:47,713 ./src/formats/mmcifformat.cpp:640:14: note: here 2025-09-09T00:49:47,713 640 | case CIFTagID::_atom_site_type_symbol: 2025-09-09T00:49:47,713 | ^~~~ 2025-09-09T00:49:50,123 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:49:50,123 from include/openbabel/mol.h:37: 2025-09-09T00:49:50,123 /usr/include/c++/14/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> >]’: 2025-09-09T00:49:50,123 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-09T00:49:50,123 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:49:50,123 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:54,269 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:49:54,269 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> >]’, 2025-09-09T00:49:54,269 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:846:41: 2025-09-09T00:49:54,269 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:49:54,269 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:49:54,269 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:54,269 514 | std::tuple(__k), 2025-09-09T00:49:54,270 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:54,270 515 | std::tuple<>()); 2025-09-09T00:49:54,270 | ~~~~~~~~~~~~~~~ 2025-09-09T00:49:54,274 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> >]’, 2025-09-09T00:49:54,275 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:981:66: 2025-09-09T00:49:54,275 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-09T00:49:54,275 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:49:54,275 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:54,275 514 | std::tuple(__k), 2025-09-09T00:49:54,275 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:54,275 515 | std::tuple<>()); 2025-09-09T00:49:54,275 | ~~~~~~~~~~~~~~~ 2025-09-09T00:49:56,366 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mmcifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:56,366 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mmcifformat.o /tmp/ccgR22pJ.s 2025-09-09T00:49:56,370 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:57,243 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:49:57,243 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:49:57,243 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mmcifformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mmcifformat.' 2025-09-09T00:49:57,246 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mmodformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mmodformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:49:57,250 Using built-in specs. 2025-09-09T00:49:57,251 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:57,251 Target: arm-linux-gnueabihf 2025-09-09T00:49:57,251 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:49:57,252 Thread model: posix 2025-09-09T00:49:57,252 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:57,252 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:57,252 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mmodformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:49:57,254 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mmodformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mmodformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc79ZqSw.s 2025-09-09T00:49:57,264 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:57,265 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:49:57,265 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:57,265 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:57,266 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:57,266 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:57,267 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:57,267 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:57,267 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:57,267 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:57,267 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:57,268 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:57,268 #include "..." search starts here: 2025-09-09T00:49:57,268 #include <...> search starts here: 2025-09-09T00:49:57,268 /usr/include/eigen3 2025-09-09T00:49:57,268 include 2025-09-09T00:49:57,269 /usr/include/python3.13 2025-09-09T00:49:57,269 /usr/include/c++/14 2025-09-09T00:49:57,269 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:57,269 /usr/include/c++/14/backward 2025-09-09T00:49:57,269 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:57,270 /usr/local/include 2025-09-09T00:49:57,270 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:57,270 /usr/include 2025-09-09T00:49:57,270 End of search list. 2025-09-09T00:49:57,291 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:58,791 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:58,791 from include/openbabel/mol.h:43, 2025-09-09T00:49:58,791 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:58,791 from ./src/formats/mmodformat.cpp:17: 2025-09-09T00:49:58,791 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:58,791 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:58,792 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:58,792 | ^ 2025-09-09T00:49:58,792 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:58,792 37 | # define UNUSED(x) x 2025-09-09T00:49:58,792 | ^ 2025-09-09T00:49:59,404 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:59,404 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:59,405 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:59,405 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:59,405 | ^ 2025-09-09T00:49:59,405 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:59,405 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:59,405 | ^~~~~~~~ 2025-09-09T00:49:59,409 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:59,409 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:59,409 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:59,409 | ^ 2025-09-09T00:49:59,410 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:59,410 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:59,410 | ^~~~~~~~ 2025-09-09T00:49:59,425 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:59,425 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:59,426 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:59,426 | ^ 2025-09-09T00:49:59,426 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:59,426 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:59,426 | ^~~~~~~~ 2025-09-09T00:49:59,433 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:59,433 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:59,433 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:59,433 | ^ 2025-09-09T00:49:59,434 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:59,434 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:59,434 | ^~~~~~~~ 2025-09-09T00:49:59,574 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:59,575 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:59,575 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:59,575 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:59,575 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:59,575 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:59,575 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:59,576 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:59,576 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:59,576 from include/openbabel/mol.h:35: 2025-09-09T00:49:59,576 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:59,576 131 | struct binary_function 2025-09-09T00:49:59,576 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:02,686 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mmodformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:02,687 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mmodformat.o /tmp/cc79ZqSw.s 2025-09-09T00:50:02,692 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:02,948 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:02,949 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:02,949 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mmodformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mmodformat.' 2025-09-09T00:50:02,951 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mol2format.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mol2format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:02,955 Using built-in specs. 2025-09-09T00:50:02,956 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:02,956 Target: arm-linux-gnueabihf 2025-09-09T00:50:02,956 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:02,957 Thread model: posix 2025-09-09T00:50:02,957 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:02,957 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:02,957 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mol2format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:02,959 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mol2format.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mol2format.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc3ZGgpB.s 2025-09-09T00:50:02,972 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:02,972 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:02,973 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:02,973 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:02,974 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:02,974 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:02,974 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:02,974 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:02,975 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:02,975 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:02,975 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:02,975 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:02,975 #include "..." search starts here: 2025-09-09T00:50:02,976 #include <...> search starts here: 2025-09-09T00:50:02,976 /usr/include/eigen3 2025-09-09T00:50:02,976 include 2025-09-09T00:50:02,976 /usr/include/python3.13 2025-09-09T00:50:02,976 /usr/include/c++/14 2025-09-09T00:50:02,977 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:02,977 /usr/include/c++/14/backward 2025-09-09T00:50:02,977 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:02,977 /usr/local/include 2025-09-09T00:50:02,977 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:02,978 /usr/include 2025-09-09T00:50:02,978 End of search list. 2025-09-09T00:50:02,997 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:04,505 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:04,505 from include/openbabel/mol.h:43, 2025-09-09T00:50:04,505 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:04,505 from ./src/formats/mol2format.cpp:17: 2025-09-09T00:50:04,505 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:04,505 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:04,506 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:04,506 | ^ 2025-09-09T00:50:04,506 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:04,506 37 | # define UNUSED(x) x 2025-09-09T00:50:04,506 | ^ 2025-09-09T00:50:05,119 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:05,119 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:05,119 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:05,119 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:05,119 | ^ 2025-09-09T00:50:05,119 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:05,119 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:05,120 | ^~~~~~~~ 2025-09-09T00:50:05,123 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:05,124 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:05,124 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:05,124 | ^ 2025-09-09T00:50:05,124 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:05,124 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:05,124 | ^~~~~~~~ 2025-09-09T00:50:05,139 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:05,139 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:05,139 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:05,139 | ^ 2025-09-09T00:50:05,140 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:05,140 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:05,140 | ^~~~~~~~ 2025-09-09T00:50:05,145 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:05,145 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:05,145 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:05,145 | ^ 2025-09-09T00:50:05,145 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:05,146 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:05,146 | ^~~~~~~~ 2025-09-09T00:50:05,285 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:05,285 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:05,285 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:05,285 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:05,285 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:05,285 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:05,285 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:05,286 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:05,286 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:05,286 from include/openbabel/mol.h:35: 2025-09-09T00:50:05,286 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:05,286 131 | struct binary_function 2025-09-09T00:50:05,287 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:05,450 ./src/formats/mol2format.cpp: In member function ‘virtual const char* OpenBabel::MOL2Format::Description()’: 2025-09-09T00:50:05,451 ./src/formats/mol2format.cpp:49:9: warning: statement has no effect [-Wunused-value] 2025-09-09T00:50:05,451 49 | " c Write UCSF Dock scores saved in comments preceeding molecules\n\n"; 2025-09-09T00:50:05,451 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:05,477 ./src/formats/mol2format.cpp: In member function ‘virtual bool OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:05,477 ./src/formats/mol2format.cpp:391:46: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:50:05,477 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2025-09-09T00:50:05,477 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:50:05,478 ./src/formats/mol2format.cpp:391:87: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:50:05,478 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2025-09-09T00:50:05,478 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:50:05,479 ./src/formats/mol2format.cpp:394:51: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:50:05,479 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2025-09-09T00:50:05,479 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:50:05,479 ./src/formats/mol2format.cpp:394:92: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:50:05,479 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2025-09-09T00:50:05,480 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:50:05,483 ./src/formats/mol2format.cpp:476:99: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:50:05,483 476 | if (n_h_bonded < min_n_h_bonded || (n_h_bonded == min_n_h_bonded && partner->GetIdx() < min_idx)) { 2025-09-09T00:50:05,484 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:50:05,485 ./src/formats/mol2format.cpp:499:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:50:05,485 499 | if (partner->GetIdx() == min_idx) { 2025-09-09T00:50:05,485 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:50:05,520 ./src/formats/mol2format.cpp: In member function ‘virtual int OpenBabel::MOL2Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:50:05,520 ./src/formats/mol2format.cpp:727:10: warning: unused variable ‘ch’ [-Wunused-variable] 2025-09-09T00:50:05,521 727 | char ch = ifs.peek(); 2025-09-09T00:50:05,521 | ^~ 2025-09-09T00:50:07,750 ./src/formats/mol2format.cpp: In member function ‘virtual bool OpenBabel::MOL2Format::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:07,750 ./src/formats/mol2format.cpp:677:40: warning: ‘%-6s’ directive output may be truncated writing between 6 and 32767 bytes into a region of size between 32756 and 32760 [-Wformat-truncation=] 2025-09-09T00:50:07,750 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:50:07,750 | ^~~~ 2025-09-09T00:50:07,750 678 | atom->GetIdx(),label, 2025-09-09T00:50:07,750 | ~~~~~ 2025-09-09T00:50:07,751 ./src/formats/mol2format.cpp:677:17: note: ‘snprintf’ output 77 or more bytes (assuming 32838) into a destination of size 32768 2025-09-09T00:50:07,751 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:50:07,751 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:07,751 678 | atom->GetIdx(),label, 2025-09-09T00:50:07,751 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:07,751 679 | atom->GetX(),atom->GetY(),atom->GetZ(), 2025-09-09T00:50:07,751 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:07,752 680 | str1.c_str(), 2025-09-09T00:50:07,752 | ~~~~~~~~~~~~~ 2025-09-09T00:50:07,752 681 | rnum,rlabel, 2025-09-09T00:50:07,752 | ~~~~~~~~~~~~ 2025-09-09T00:50:07,752 682 | atom->GetPartialCharge()); 2025-09-09T00:50:07,752 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:07,752 ./src/formats/mol2format.cpp:677:40: warning: ‘%-6s’ directive output may be truncated writing between 6 and 32767 bytes into a region of size between 32756 and 32760 [-Wformat-truncation=] 2025-09-09T00:50:07,753 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:50:07,753 | ^~~~ 2025-09-09T00:50:07,753 678 | atom->GetIdx(),label, 2025-09-09T00:50:07,753 | ~~~~~ 2025-09-09T00:50:07,753 ./src/formats/mol2format.cpp:677:17: note: ‘snprintf’ output 77 or more bytes (assuming 32838) into a destination of size 32768 2025-09-09T00:50:07,753 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:50:07,753 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:07,753 678 | atom->GetIdx(),label, 2025-09-09T00:50:07,754 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:07,754 679 | atom->GetX(),atom->GetY(),atom->GetZ(), 2025-09-09T00:50:07,754 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:07,754 680 | str1.c_str(), 2025-09-09T00:50:07,754 | ~~~~~~~~~~~~~ 2025-09-09T00:50:07,754 681 | rnum,rlabel, 2025-09-09T00:50:07,754 | ~~~~~~~~~~~~ 2025-09-09T00:50:07,754 682 | atom->GetPartialCharge()); 2025-09-09T00:50:07,754 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:10,625 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mol2format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:10,626 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mol2format.o /tmp/cc3ZGgpB.s 2025-09-09T00:50:10,631 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:11,053 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:11,053 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:11,054 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mol2format.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mol2format.' 2025-09-09T00:50:11,056 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/moldenformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/moldenformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:11,060 Using built-in specs. 2025-09-09T00:50:11,061 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:11,061 Target: arm-linux-gnueabihf 2025-09-09T00:50:11,062 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:11,062 Thread model: posix 2025-09-09T00:50:11,062 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:11,062 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:11,062 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/moldenformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:11,064 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/moldenformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase moldenformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccYEmRvY.s 2025-09-09T00:50:11,075 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:11,075 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:11,076 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:11,076 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:11,077 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:11,077 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:11,077 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:11,078 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:11,078 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:11,078 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:11,078 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:11,078 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:11,079 #include "..." search starts here: 2025-09-09T00:50:11,079 #include <...> search starts here: 2025-09-09T00:50:11,079 /usr/include/eigen3 2025-09-09T00:50:11,079 include 2025-09-09T00:50:11,080 /usr/include/python3.13 2025-09-09T00:50:11,080 /usr/include/c++/14 2025-09-09T00:50:11,080 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:11,080 /usr/include/c++/14/backward 2025-09-09T00:50:11,080 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:11,080 /usr/local/include 2025-09-09T00:50:11,081 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:11,081 /usr/include 2025-09-09T00:50:11,081 End of search list. 2025-09-09T00:50:11,100 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:12,567 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:12,567 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:12,567 from ./src/formats/moldenformat.cpp:35: 2025-09-09T00:50:12,567 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:12,567 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:12,567 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:12,568 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:50:12,568 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:50:12,568 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:50:12,568 from /usr/include/c++/14/ios:44, 2025-09-09T00:50:12,568 from /usr/include/c++/14/istream:40, 2025-09-09T00:50:12,568 from /usr/include/c++/14/fstream:40, 2025-09-09T00:50:12,569 from ./src/formats/moldenformat.cpp:27: 2025-09-09T00:50:12,569 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:12,569 131 | struct binary_function 2025-09-09T00:50:12,569 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:12,739 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:12,740 from include/openbabel/mol.h:43, 2025-09-09T00:50:12,740 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:12,740 from ./src/formats/moldenformat.cpp:36: 2025-09-09T00:50:12,740 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:12,740 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:12,740 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:12,740 | ^ 2025-09-09T00:50:12,740 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:12,741 37 | # define UNUSED(x) x 2025-09-09T00:50:12,741 | ^ 2025-09-09T00:50:13,286 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:13,287 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:13,287 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:13,287 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:13,287 | ^ 2025-09-09T00:50:13,287 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:13,287 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:13,287 | ^~~~~~~~ 2025-09-09T00:50:13,291 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:13,291 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:13,292 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:13,292 | ^ 2025-09-09T00:50:13,292 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:13,292 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:13,292 | ^~~~~~~~ 2025-09-09T00:50:13,307 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:13,307 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:13,307 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:13,307 | ^ 2025-09-09T00:50:13,307 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:13,307 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:13,308 | ^~~~~~~~ 2025-09-09T00:50:13,313 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:13,313 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:13,313 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:13,313 | ^ 2025-09-09T00:50:13,313 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:13,313 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:13,313 | ^~~~~~~~ 2025-09-09T00:50:13,521 ./src/formats/moldenformat.cpp: In member function ‘virtual int OpenBabel::OBMoldenFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:50:13,521 ./src/formats/moldenformat.cpp:85:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:50:13,521 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:50:13,521 | ~~~~^ 2025-09-09T00:50:13,521 ./src/formats/moldenformat.cpp:85:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:50:13,521 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:50:13,521 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:50:13,531 ./src/formats/moldenformat.cpp: In member function ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:13,532 ./src/formats/moldenformat.cpp:171:48: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:50:13,532 171 | if (sscanf(lineBuffer.c_str(), "%d", &natoms) == 0 || !natoms) { 2025-09-09T00:50:13,532 | ~^ ~~~~~~~ 2025-09-09T00:50:13,532 | | | 2025-09-09T00:50:13,532 | | unsigned int* 2025-09-09T00:50:13,532 | int* 2025-09-09T00:50:13,532 | %d 2025-09-09T00:50:20,160 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/moldenformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:20,161 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/moldenformat.o /tmp/ccYEmRvY.s 2025-09-09T00:50:20,169 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:20,750 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:20,750 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:20,750 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/moldenformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/moldenformat.' 2025-09-09T00:50:20,751 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/molproformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/molproformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:20,755 Using built-in specs. 2025-09-09T00:50:20,756 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:20,756 Target: arm-linux-gnueabihf 2025-09-09T00:50:20,756 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:20,757 Thread model: posix 2025-09-09T00:50:20,757 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:20,757 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:20,757 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/molproformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:20,759 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/molproformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase molproformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccAftq4e.s 2025-09-09T00:50:20,769 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:20,769 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:20,770 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:20,770 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:20,771 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:20,771 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:20,772 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:20,772 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:20,772 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:20,772 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:20,772 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:20,773 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:20,773 #include "..." search starts here: 2025-09-09T00:50:20,773 #include <...> search starts here: 2025-09-09T00:50:20,773 /usr/include/eigen3 2025-09-09T00:50:20,773 include 2025-09-09T00:50:20,774 /usr/include/python3.13 2025-09-09T00:50:20,774 /usr/include/c++/14 2025-09-09T00:50:20,774 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:20,774 /usr/include/c++/14/backward 2025-09-09T00:50:20,774 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:20,774 /usr/local/include 2025-09-09T00:50:20,775 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:20,775 /usr/include 2025-09-09T00:50:20,775 End of search list. 2025-09-09T00:50:20,795 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:22,303 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:22,303 from include/openbabel/mol.h:43, 2025-09-09T00:50:22,303 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:22,303 from ./src/formats/molproformat.cpp:20: 2025-09-09T00:50:22,303 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:22,304 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:22,304 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:22,304 | ^ 2025-09-09T00:50:22,304 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:22,304 37 | # define UNUSED(x) x 2025-09-09T00:50:22,304 | ^ 2025-09-09T00:50:22,923 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:22,923 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:22,923 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:22,923 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:22,923 | ^ 2025-09-09T00:50:22,924 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:22,924 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:22,924 | ^~~~~~~~ 2025-09-09T00:50:22,928 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:22,928 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:22,928 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:22,928 | ^ 2025-09-09T00:50:22,928 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:22,928 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:22,929 | ^~~~~~~~ 2025-09-09T00:50:22,943 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:22,943 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:22,943 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:22,944 | ^ 2025-09-09T00:50:22,944 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:22,944 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:22,944 | ^~~~~~~~ 2025-09-09T00:50:22,949 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:22,949 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:22,949 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:22,950 | ^ 2025-09-09T00:50:22,950 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:22,950 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:22,950 | ^~~~~~~~ 2025-09-09T00:50:23,089 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:23,089 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:23,089 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:23,089 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:23,089 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:23,089 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:23,089 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:23,090 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:23,090 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:23,090 from include/openbabel/mol.h:35: 2025-09-09T00:50:23,090 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:23,090 131 | struct binary_function 2025-09-09T00:50:23,091 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:27,973 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/molproformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:27,974 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/molproformat.o /tmp/ccAftq4e.s 2025-09-09T00:50:27,979 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:28,401 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:28,401 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:28,402 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/molproformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/molproformat.' 2025-09-09T00:50:28,404 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/molreport.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/molreport.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:28,408 Using built-in specs. 2025-09-09T00:50:28,409 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:28,409 Target: arm-linux-gnueabihf 2025-09-09T00:50:28,410 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:28,410 Thread model: posix 2025-09-09T00:50:28,410 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:28,410 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:28,411 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/molreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:28,412 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/molreport.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase molreport.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cchLq3Pl.s 2025-09-09T00:50:28,427 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:28,427 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:28,428 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:28,428 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:28,429 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:28,429 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:28,429 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:28,429 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:28,430 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:28,430 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:28,430 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:28,430 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:28,431 #include "..." search starts here: 2025-09-09T00:50:28,431 #include <...> search starts here: 2025-09-09T00:50:28,431 /usr/include/eigen3 2025-09-09T00:50:28,431 include 2025-09-09T00:50:28,431 /usr/include/python3.13 2025-09-09T00:50:28,431 /usr/include/c++/14 2025-09-09T00:50:28,432 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:28,432 /usr/include/c++/14/backward 2025-09-09T00:50:28,432 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:28,432 /usr/local/include 2025-09-09T00:50:28,432 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:28,433 /usr/include 2025-09-09T00:50:28,433 End of search list. 2025-09-09T00:50:28,449 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:29,935 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:29,935 from include/openbabel/mol.h:43, 2025-09-09T00:50:29,935 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:29,935 from ./src/formats/molreport.cpp:21: 2025-09-09T00:50:29,935 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:29,935 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:29,936 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:29,936 | ^ 2025-09-09T00:50:29,936 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:29,936 37 | # define UNUSED(x) x 2025-09-09T00:50:29,936 | ^ 2025-09-09T00:50:30,546 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:30,546 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:30,546 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:30,546 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:30,546 | ^ 2025-09-09T00:50:30,546 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:30,546 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:30,546 | ^~~~~~~~ 2025-09-09T00:50:30,550 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:30,551 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:30,551 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:30,551 | ^ 2025-09-09T00:50:30,551 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:30,551 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:30,551 | ^~~~~~~~ 2025-09-09T00:50:30,566 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:30,566 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:30,566 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:30,566 | ^ 2025-09-09T00:50:30,566 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:30,566 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:30,567 | ^~~~~~~~ 2025-09-09T00:50:30,572 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:30,572 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:30,572 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:30,572 | ^ 2025-09-09T00:50:30,572 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:30,573 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:30,573 | ^~~~~~~~ 2025-09-09T00:50:30,711 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:30,711 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:30,711 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:30,711 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:30,711 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:30,711 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:30,711 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:30,712 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:30,712 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:30,713 from include/openbabel/mol.h:35: 2025-09-09T00:50:30,713 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:30,713 131 | struct binary_function 2025-09-09T00:50:30,713 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:32,717 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/molreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:32,718 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/molreport.o /tmp/cchLq3Pl.s 2025-09-09T00:50:32,723 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:32,881 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:32,881 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:32,881 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/molreport.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/molreport.' 2025-09-09T00:50:32,883 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mopacformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mopacformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:32,887 Using built-in specs. 2025-09-09T00:50:32,888 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:32,888 Target: arm-linux-gnueabihf 2025-09-09T00:50:32,889 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:32,889 Thread model: posix 2025-09-09T00:50:32,889 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:32,889 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:32,890 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mopacformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:32,891 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mopacformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mopacformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc2KNo28.s 2025-09-09T00:50:32,904 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:32,904 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:32,905 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:32,905 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:32,906 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:32,906 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:32,906 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:32,906 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:32,907 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:32,907 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:32,907 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:32,907 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:32,907 #include "..." search starts here: 2025-09-09T00:50:32,908 #include <...> search starts here: 2025-09-09T00:50:32,908 /usr/include/eigen3 2025-09-09T00:50:32,908 include 2025-09-09T00:50:32,908 /usr/include/python3.13 2025-09-09T00:50:32,908 /usr/include/c++/14 2025-09-09T00:50:32,908 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:32,909 /usr/include/c++/14/backward 2025-09-09T00:50:32,909 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:32,909 /usr/local/include 2025-09-09T00:50:32,909 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:32,909 /usr/include 2025-09-09T00:50:32,909 End of search list. 2025-09-09T00:50:32,926 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:34,418 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:34,418 from include/openbabel/mol.h:43, 2025-09-09T00:50:34,418 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:34,418 from ./src/formats/mopacformat.cpp:17: 2025-09-09T00:50:34,418 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:34,419 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:34,419 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:34,419 | ^ 2025-09-09T00:50:34,419 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:34,419 37 | # define UNUSED(x) x 2025-09-09T00:50:34,419 | ^ 2025-09-09T00:50:35,031 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:35,031 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:35,031 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:35,031 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:35,031 | ^ 2025-09-09T00:50:35,031 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:35,031 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:35,032 | ^~~~~~~~ 2025-09-09T00:50:35,035 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:35,036 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:35,036 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:35,036 | ^ 2025-09-09T00:50:35,036 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:35,036 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:35,036 | ^~~~~~~~ 2025-09-09T00:50:35,051 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:35,051 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:35,051 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:35,051 | ^ 2025-09-09T00:50:35,052 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:35,052 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:35,052 | ^~~~~~~~ 2025-09-09T00:50:35,057 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:35,057 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:35,057 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:35,057 | ^ 2025-09-09T00:50:35,057 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:35,058 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:35,058 | ^~~~~~~~ 2025-09-09T00:50:35,197 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:35,197 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:35,197 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:35,197 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:35,197 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:35,197 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:35,197 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:35,198 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:35,198 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:35,198 from include/openbabel/mol.h:35: 2025-09-09T00:50:35,198 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:35,198 131 | struct binary_function 2025-09-09T00:50:35,199 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:35,411 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACCARTFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:35,411 ./src/formats/mopacformat.cpp:642:19: warning: variable ‘isotopeMass’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:50:35,412 642 | double x,y,z, isotopeMass; 2025-09-09T00:50:35,412 | ^~~~~~~~~~~ 2025-09-09T00:50:41,384 In file included from include/openbabel/atom.h:35: 2025-09-09T00:50:41,384 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2025-09-09T00:50:41,384 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2025-09-09T00:50:41,384 include/openbabel/math/vector3.h:90:11: warning: ‘x’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:50:41,385 90 | _vx = inX; 2025-09-09T00:50:41,385 | ~~~~^~~~~ 2025-09-09T00:50:41,385 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:41,385 ./src/formats/mopacformat.cpp:73:12: note: ‘x’ was declared here 2025-09-09T00:50:41,385 73 | double x,y,z; 2025-09-09T00:50:41,385 | ^ 2025-09-09T00:50:41,386 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2025-09-09T00:50:41,386 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2025-09-09T00:50:41,386 include/openbabel/math/vector3.h:91:11: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:50:41,386 91 | _vy = inY; 2025-09-09T00:50:41,386 | ~~~~^~~~~ 2025-09-09T00:50:41,386 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:41,386 ./src/formats/mopacformat.cpp:73:14: note: ‘y’ was declared here 2025-09-09T00:50:41,386 73 | double x,y,z; 2025-09-09T00:50:41,387 | ^ 2025-09-09T00:50:43,881 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mopacformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:43,882 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mopacformat.o /tmp/cc2KNo28.s 2025-09-09T00:50:43,887 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:44,610 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:44,610 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:44,611 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mopacformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mopacformat.' 2025-09-09T00:50:44,614 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mpdformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mpdformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:44,618 Using built-in specs. 2025-09-09T00:50:44,619 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:44,619 Target: arm-linux-gnueabihf 2025-09-09T00:50:44,620 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:44,620 Thread model: posix 2025-09-09T00:50:44,620 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:44,620 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:44,621 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mpdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:44,622 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mpdformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mpdformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccGdSqee.s 2025-09-09T00:50:44,632 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:44,633 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:44,633 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:44,633 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:44,635 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:44,635 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:44,635 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:44,636 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:44,636 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:44,636 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:44,636 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:44,636 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:44,637 #include "..." search starts here: 2025-09-09T00:50:44,637 #include <...> search starts here: 2025-09-09T00:50:44,637 /usr/include/eigen3 2025-09-09T00:50:44,638 include 2025-09-09T00:50:44,638 /usr/include/python3.13 2025-09-09T00:50:44,638 /usr/include/c++/14 2025-09-09T00:50:44,638 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:44,638 /usr/include/c++/14/backward 2025-09-09T00:50:44,638 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:44,639 /usr/local/include 2025-09-09T00:50:44,639 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:44,639 /usr/include 2025-09-09T00:50:44,639 End of search list. 2025-09-09T00:50:44,658 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:46,159 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:46,159 from include/openbabel/mol.h:43, 2025-09-09T00:50:46,159 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:46,159 from ./src/formats/mpdformat.cpp:22: 2025-09-09T00:50:46,159 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:46,159 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:46,160 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:46,160 | ^ 2025-09-09T00:50:46,160 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:46,160 37 | # define UNUSED(x) x 2025-09-09T00:50:46,160 | ^ 2025-09-09T00:50:46,782 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:46,782 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:46,782 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:46,783 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:46,783 | ^ 2025-09-09T00:50:46,783 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:46,783 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:46,783 | ^~~~~~~~ 2025-09-09T00:50:46,787 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:46,787 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:46,787 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:46,787 | ^ 2025-09-09T00:50:46,788 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:46,788 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:46,788 | ^~~~~~~~ 2025-09-09T00:50:46,802 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:46,803 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:46,803 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:46,803 | ^ 2025-09-09T00:50:46,803 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:46,803 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:46,803 | ^~~~~~~~ 2025-09-09T00:50:46,808 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:46,808 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:46,809 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:46,809 | ^ 2025-09-09T00:50:46,809 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:46,809 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:46,809 | ^~~~~~~~ 2025-09-09T00:50:46,948 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:46,948 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:46,948 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:46,948 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:46,948 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:46,948 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:46,949 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:46,949 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:46,950 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:46,950 from include/openbabel/mol.h:35: 2025-09-09T00:50:46,950 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:46,950 131 | struct binary_function 2025-09-09T00:50:46,950 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:47,132 ./src/formats/mpdformat.cpp: In member function ‘virtual bool OpenBabel::MPDFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:47,132 ./src/formats/mpdformat.cpp:204:42: warning: variable ‘idx_true’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:50:47,133 204 | bool xml_true=false, pre_true=false, idx_true=false; 2025-09-09T00:50:47,133 | ^~~~~~~~ 2025-09-09T00:50:49,340 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mpdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:49,341 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mpdformat.o /tmp/ccGdSqee.s 2025-09-09T00:50:49,346 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:49,552 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:49,553 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:49,553 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mpdformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mpdformat.' 2025-09-09T00:50:49,555 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/mpqcformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mpqcformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:49,558 Using built-in specs. 2025-09-09T00:50:49,559 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:49,560 Target: arm-linux-gnueabihf 2025-09-09T00:50:49,560 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:49,560 Thread model: posix 2025-09-09T00:50:49,560 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:49,561 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:49,561 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mpqcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:49,563 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/mpqcformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase mpqcformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccBlfOan.s 2025-09-09T00:50:49,572 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:49,573 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:49,573 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:49,573 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:49,574 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:49,574 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:49,574 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:49,574 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:49,575 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:49,575 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:49,575 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:49,575 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:49,575 #include "..." search starts here: 2025-09-09T00:50:49,576 #include <...> search starts here: 2025-09-09T00:50:49,576 /usr/include/eigen3 2025-09-09T00:50:49,576 include 2025-09-09T00:50:49,576 /usr/include/python3.13 2025-09-09T00:50:49,576 /usr/include/c++/14 2025-09-09T00:50:49,577 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:49,577 /usr/include/c++/14/backward 2025-09-09T00:50:49,577 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:49,577 /usr/local/include 2025-09-09T00:50:49,577 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:49,578 /usr/include 2025-09-09T00:50:49,578 End of search list. 2025-09-09T00:50:49,598 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:51,103 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:51,104 from include/openbabel/mol.h:43, 2025-09-09T00:50:51,104 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:51,104 from ./src/formats/mpqcformat.cpp:16: 2025-09-09T00:50:51,104 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:51,104 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:51,104 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:51,104 | ^ 2025-09-09T00:50:51,104 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:51,104 37 | # define UNUSED(x) x 2025-09-09T00:50:51,105 | ^ 2025-09-09T00:50:51,723 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:51,723 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:51,723 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:51,723 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:51,723 | ^ 2025-09-09T00:50:51,723 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:51,724 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:51,724 | ^~~~~~~~ 2025-09-09T00:50:51,728 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:51,728 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:51,728 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:51,728 | ^ 2025-09-09T00:50:51,728 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:51,728 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:51,728 | ^~~~~~~~ 2025-09-09T00:50:51,743 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:51,743 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:51,743 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:51,743 | ^ 2025-09-09T00:50:51,744 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:51,744 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:51,744 | ^~~~~~~~ 2025-09-09T00:50:51,749 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:51,749 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:51,749 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:51,749 | ^ 2025-09-09T00:50:51,750 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:51,750 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:51,750 | ^~~~~~~~ 2025-09-09T00:50:51,888 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:51,888 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:51,888 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:51,888 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:51,889 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:51,889 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:51,889 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:51,890 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:51,890 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:51,890 from include/openbabel/mol.h:35: 2025-09-09T00:50:51,890 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:51,890 131 | struct binary_function 2025-09-09T00:50:51,890 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:54,142 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mpqcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:54,143 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/mpqcformat.o /tmp/ccBlfOan.s 2025-09-09T00:50:54,148 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:54,328 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:54,328 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:54,329 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/mpqcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/mpqcformat.' 2025-09-09T00:50:54,330 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/msiformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/msiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:54,334 Using built-in specs. 2025-09-09T00:50:54,335 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:54,335 Target: arm-linux-gnueabihf 2025-09-09T00:50:54,336 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:54,336 Thread model: posix 2025-09-09T00:50:54,336 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:54,336 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:54,337 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/msiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:54,338 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/msiformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase msiformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc3FmHRW.s 2025-09-09T00:50:54,349 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:54,349 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:54,349 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:54,350 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:54,350 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:54,351 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:54,351 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:54,351 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:54,351 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:54,351 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:54,351 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:54,352 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:54,352 #include "..." search starts here: 2025-09-09T00:50:54,352 #include <...> search starts here: 2025-09-09T00:50:54,352 /usr/include/eigen3 2025-09-09T00:50:54,352 include 2025-09-09T00:50:54,352 /usr/include/python3.13 2025-09-09T00:50:54,352 /usr/include/c++/14 2025-09-09T00:50:54,353 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:54,353 /usr/include/c++/14/backward 2025-09-09T00:50:54,353 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:54,353 /usr/local/include 2025-09-09T00:50:54,353 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:54,353 /usr/include 2025-09-09T00:50:54,353 End of search list. 2025-09-09T00:50:54,370 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:55,865 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:55,865 from include/openbabel/mol.h:43, 2025-09-09T00:50:55,865 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:55,865 from ./src/formats/msiformat.cpp:15: 2025-09-09T00:50:55,866 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:55,866 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:55,866 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:55,866 | ^ 2025-09-09T00:50:55,866 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:55,866 37 | # define UNUSED(x) x 2025-09-09T00:50:55,866 | ^ 2025-09-09T00:50:56,482 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:56,482 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,482 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,482 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:56,482 | ^ 2025-09-09T00:50:56,482 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:56,482 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:56,482 | ^~~~~~~~ 2025-09-09T00:50:56,486 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,487 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,487 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:56,487 | ^ 2025-09-09T00:50:56,487 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:56,487 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:56,487 | ^~~~~~~~ 2025-09-09T00:50:56,502 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,502 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,502 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:56,502 | ^ 2025-09-09T00:50:56,502 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:56,502 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:56,503 | ^~~~~~~~ 2025-09-09T00:50:56,508 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,508 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,508 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:56,508 | ^ 2025-09-09T00:50:56,508 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:56,508 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:56,508 | ^~~~~~~~ 2025-09-09T00:50:56,646 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:56,647 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:56,647 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:56,647 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:56,647 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:56,647 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:56,647 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:56,648 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:56,648 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:56,648 from include/openbabel/mol.h:35: 2025-09-09T00:50:56,648 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:56,648 131 | struct binary_function 2025-09-09T00:50:56,648 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:56,822 ./src/formats/msiformat.cpp: In member function ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:56,822 ./src/formats/msiformat.cpp:71:17: warning: unused variable ‘title’ [-Wunused-variable] 2025-09-09T00:50:56,822 71 | const char* title = pConv->GetTitle(); 2025-09-09T00:50:56,822 | ^~~~~ 2025-09-09T00:50:59,426 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/msiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:59,427 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/msiformat.o /tmp/cc3FmHRW.s 2025-09-09T00:50:59,432 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:59,677 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:50:59,677 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:50:59,677 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/msiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/msiformat.' 2025-09-09T00:50:59,679 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/msmsformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/msmsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:59,683 Using built-in specs. 2025-09-09T00:50:59,684 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:59,684 Target: arm-linux-gnueabihf 2025-09-09T00:50:59,685 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:50:59,685 Thread model: posix 2025-09-09T00:50:59,685 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:59,685 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:59,686 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/msmsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:50:59,687 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/msmsformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase msmsformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc0wbfIc.s 2025-09-09T00:50:59,697 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:59,697 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:50:59,698 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:59,698 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:59,699 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:59,699 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:59,699 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:59,699 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:59,700 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:59,700 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:59,700 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:59,700 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:59,700 #include "..." search starts here: 2025-09-09T00:50:59,701 #include <...> search starts here: 2025-09-09T00:50:59,701 /usr/include/eigen3 2025-09-09T00:50:59,701 include 2025-09-09T00:50:59,701 /usr/include/python3.13 2025-09-09T00:50:59,701 /usr/include/c++/14 2025-09-09T00:50:59,702 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:59,702 /usr/include/c++/14/backward 2025-09-09T00:50:59,702 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:59,702 /usr/local/include 2025-09-09T00:50:59,702 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:59,702 /usr/include 2025-09-09T00:50:59,703 End of search list. 2025-09-09T00:50:59,723 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:01,221 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:01,221 from include/openbabel/mol.h:43, 2025-09-09T00:51:01,221 from ./src/formats/msmsformat.cpp:26: 2025-09-09T00:51:01,221 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:01,221 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:01,221 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:01,221 | ^ 2025-09-09T00:51:01,221 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:01,221 37 | # define UNUSED(x) x 2025-09-09T00:51:01,221 | ^ 2025-09-09T00:51:01,833 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:01,833 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:01,833 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:01,834 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:01,834 | ^ 2025-09-09T00:51:01,834 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:01,834 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:01,834 | ^~~~~~~~ 2025-09-09T00:51:01,838 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:01,838 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:01,838 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:01,838 | ^ 2025-09-09T00:51:01,839 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:01,839 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:01,839 | ^~~~~~~~ 2025-09-09T00:51:01,853 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:01,854 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:01,854 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:01,854 | ^ 2025-09-09T00:51:01,854 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:01,854 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:01,854 | ^~~~~~~~ 2025-09-09T00:51:01,859 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:01,860 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:01,860 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:01,860 | ^ 2025-09-09T00:51:01,860 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:01,860 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:01,860 | ^~~~~~~~ 2025-09-09T00:51:01,999 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:01,999 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:01,999 from ./src/formats/msmsformat.cpp:27: 2025-09-09T00:51:01,999 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:01,999 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:01,999 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:01,999 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:02,000 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:02,000 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:02,000 from include/openbabel/mol.h:35: 2025-09-09T00:51:02,001 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:02,001 131 | struct binary_function 2025-09-09T00:51:02,001 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:02,164 ./src/formats/msmsformat.cpp: In member function ‘virtual int OpenBabel::OBMSMSFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:51:02,165 ./src/formats/msmsformat.cpp:82:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:51:02,165 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:51:02,165 | ~~~~^ 2025-09-09T00:51:02,165 ./src/formats/msmsformat.cpp:82:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:51:02,165 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:51:02,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:51:03,983 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/msmsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:03,984 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/msmsformat.o /tmp/cc0wbfIc.s 2025-09-09T00:51:03,989 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:04,142 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:04,142 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:04,143 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/msmsformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/msmsformat.' 2025-09-09T00:51:04,144 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/nulformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/nulformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:04,148 Using built-in specs. 2025-09-09T00:51:04,149 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:04,149 Target: arm-linux-gnueabihf 2025-09-09T00:51:04,150 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:04,150 Thread model: posix 2025-09-09T00:51:04,150 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:04,150 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:04,151 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/nulformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:04,152 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/nulformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase nulformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccl9G693.s 2025-09-09T00:51:04,163 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:04,163 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:04,164 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:04,164 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:04,165 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:04,165 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:04,165 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:04,165 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:04,166 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:04,166 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:04,166 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:04,166 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:04,166 #include "..." search starts here: 2025-09-09T00:51:04,167 #include <...> search starts here: 2025-09-09T00:51:04,167 /usr/include/eigen3 2025-09-09T00:51:04,167 include 2025-09-09T00:51:04,167 /usr/include/python3.13 2025-09-09T00:51:04,167 /usr/include/c++/14 2025-09-09T00:51:04,168 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:04,168 /usr/include/c++/14/backward 2025-09-09T00:51:04,168 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:04,168 /usr/local/include 2025-09-09T00:51:04,168 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:04,168 /usr/include 2025-09-09T00:51:04,169 End of search list. 2025-09-09T00:51:04,187 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:05,516 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:05,516 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:05,517 from ./src/formats/nulformat.cpp:14: 2025-09-09T00:51:05,517 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:05,517 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:05,517 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:05,517 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:51:05,518 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:51:05,518 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:51:05,518 from /usr/include/c++/14/ios:44, 2025-09-09T00:51:05,518 from /usr/include/c++/14/ostream:40, 2025-09-09T00:51:05,518 from /usr/include/c++/14/iostream:41, 2025-09-09T00:51:05,518 from include/openbabel/obconversion.h:24: 2025-09-09T00:51:05,518 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:05,518 131 | struct binary_function 2025-09-09T00:51:05,518 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:05,638 In file included from ./src/formats/nulformat.cpp:15: 2025-09-09T00:51:05,639 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:05,639 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:05,639 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:05,639 | ^ 2025-09-09T00:51:05,639 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:05,639 37 | # define UNUSED(x) x 2025-09-09T00:51:05,639 | ^ 2025-09-09T00:51:06,395 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/nulformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:06,395 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/nulformat.o /tmp/ccl9G693.s 2025-09-09T00:51:06,400 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:06,494 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:06,494 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:06,495 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/nulformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/nulformat.' 2025-09-09T00:51:06,496 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/nwchemformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/nwchemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:06,500 Using built-in specs. 2025-09-09T00:51:06,501 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:06,501 Target: arm-linux-gnueabihf 2025-09-09T00:51:06,501 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:06,501 Thread model: posix 2025-09-09T00:51:06,501 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:06,501 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:06,502 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/nwchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:06,502 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/nwchemformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase nwchemformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccUitTIZ.s 2025-09-09T00:51:06,511 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:06,511 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:06,512 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:06,512 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:06,512 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:06,512 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:06,512 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:06,512 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:06,512 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:06,513 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:06,513 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:06,513 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:06,513 #include "..." search starts here: 2025-09-09T00:51:06,513 #include <...> search starts here: 2025-09-09T00:51:06,513 /usr/include/eigen3 2025-09-09T00:51:06,513 include 2025-09-09T00:51:06,514 /usr/include/python3.13 2025-09-09T00:51:06,514 /usr/include/c++/14 2025-09-09T00:51:06,514 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:06,514 /usr/include/c++/14/backward 2025-09-09T00:51:06,514 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:06,514 /usr/local/include 2025-09-09T00:51:06,514 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:06,514 /usr/include 2025-09-09T00:51:06,514 End of search list. 2025-09-09T00:51:06,531 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:08,025 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:08,025 from include/openbabel/mol.h:43, 2025-09-09T00:51:08,025 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:08,025 from ./src/formats/nwchemformat.cpp:17: 2025-09-09T00:51:08,025 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:08,025 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:08,025 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:08,026 | ^ 2025-09-09T00:51:08,026 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:08,026 37 | # define UNUSED(x) x 2025-09-09T00:51:08,026 | ^ 2025-09-09T00:51:08,638 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:08,638 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:08,638 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:08,638 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:08,638 | ^ 2025-09-09T00:51:08,638 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:08,638 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:08,638 | ^~~~~~~~ 2025-09-09T00:51:08,641 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:08,642 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:08,642 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:08,642 | ^ 2025-09-09T00:51:08,642 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:08,642 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:08,642 | ^~~~~~~~ 2025-09-09T00:51:08,656 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:08,656 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:08,656 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:08,656 | ^ 2025-09-09T00:51:08,656 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:08,657 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:08,657 | ^~~~~~~~ 2025-09-09T00:51:08,661 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:08,661 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:08,661 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:08,661 | ^ 2025-09-09T00:51:08,662 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:08,662 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:08,662 | ^~~~~~~~ 2025-09-09T00:51:08,800 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:08,800 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:08,800 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:08,800 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:08,800 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:08,800 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:08,800 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:08,800 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:08,801 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:08,801 from include/openbabel/mol.h:35: 2025-09-09T00:51:08,801 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:08,801 131 | struct binary_function 2025-09-09T00:51:08,801 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:08,970 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:08,970 ./src/formats/nwchemformat.cpp:221:72: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:51:08,970 221 | if ((i>=natoms) || (molecule->GetAtom(i+1)->GetAtomicNum() != atoi(vs[2].c_str()))) 2025-09-09T00:51:08,970 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:08,975 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMultipoleMoment(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:08,975 ./src/formats/nwchemformat.cpp:296:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2025-09-09T00:51:08,975 296 | else if (vs[0][0] == '1') 2025-09-09T00:51:08,975 | ^ 2025-09-09T00:51:08,979 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadPartialCharges(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:08,980 ./src/formats/nwchemformat.cpp:413:56: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:51:08,980 413 | if (molecule->GetAtom(i++)->GetAtomicNum() != charge) 2025-09-09T00:51:08,980 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:51:08,988 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMEPCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:08,988 ./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] 2025-09-09T00:51:08,988 561 | if (energies.size() != molecule->NumConformers()) 2025-09-09T00:51:08,988 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:09,020 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadNEBCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:09,021 ./src/formats/nwchemformat.cpp:826:79: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:51:09,021 826 | if (etab.GetAtomicNum(vs[1].substr(0, end_of_symbol).c_str()) != molecule->GetAtom(i+1)->GetAtomicNum()) 2025-09-09T00:51:09,021 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:09,027 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:09,028 ./src/formats/nwchemformat.cpp:914:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:51:09,028 914 | if (atoi(buffer) != natoms) 2025-09-09T00:51:09,028 | ~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:51:09,028 ./src/formats/nwchemformat.cpp:924:84: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:51:09,028 924 | if ((vs.size() < 4) || (molecule->GetAtom(i+1)->GetAtomicNum() != etab.GetAtomicNum(vs[0].c_str()))) 2025-09-09T00:51:09,028 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:10,210 ./src/formats/nwchemformat.cpp: At global scope: 2025-09-09T00:51:10,211 ./src/formats/nwchemformat.cpp:104:20: warning: ‘OpenBabel::BETA_ORBITAL_PATTERN’ defined but not used [-Wunused-variable] 2025-09-09T00:51:10,211 104 | static const char* BETA_ORBITAL_PATTERN = "Beta"; 2025-09-09T00:51:10,211 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:12,799 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:12,800 ./src/formats/nwchemformat.cpp:237:18: warning: ‘coordinates’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:51:12,800 237 | delete[] coordinates; 2025-09-09T00:51:12,800 | ^~~~~~~~~~~ 2025-09-09T00:51:12,800 ./src/formats/nwchemformat.cpp:195:13: note: ‘coordinates’ was declared here 2025-09-09T00:51:12,800 195 | double* coordinates; 2025-09-09T00:51:12,800 | ^~~~~~~~~~~ 2025-09-09T00:51:13,915 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:13,915 ./src/formats/nwchemformat.cpp:939:21: warning: ‘nbeads’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:51:13,915 939 | if (bead_number != nbeads) 2025-09-09T00:51:13,915 | ^~ 2025-09-09T00:51:13,916 ./src/formats/nwchemformat.cpp:886:18: note: ‘nbeads’ was declared here 2025-09-09T00:51:13,916 886 | unsigned int nbeads; 2025-09-09T00:51:13,916 | ^~~~~~ 2025-09-09T00:51:15,603 In file included from /usr/include/c++/14/vector:65: 2025-09-09T00:51:15,604 /usr/include/c++/14/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’: 2025-09-09T00:51:15,604 /usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:15,604 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2025-09-09T00:51:15,604 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:51:15,604 /usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:15,705 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]’, 2025-09-09T00:51:15,705 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:15,705 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:15,705 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++/14/bits/stl_vector.h:1624:35, 2025-09-09T00:51:15,706 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++/14/bits/vector.tcc:238:44: 2025-09-09T00:51:15,706 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:15,706 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:15,706 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:15,812 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]’, 2025-09-09T00:51:15,812 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:15,812 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:15,812 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, 2025-09-09T00:51:15,812 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:51:15,812 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:51:15,812 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:15,812 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:15,812 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:15,813 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]’, 2025-09-09T00:51:15,813 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:15,813 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:15,813 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, 2025-09-09T00:51:15,813 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:51:15,813 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:51:15,813 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:15,813 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:15,813 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:16,172 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]’, 2025-09-09T00:51:16,172 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:16,172 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:16,172 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, 2025-09-09T00:51:16,172 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:493:43: 2025-09-09T00:51:16,172 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:16,173 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:16,173 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:16,173 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]’, 2025-09-09T00:51:16,173 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:16,173 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:16,174 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, 2025-09-09T00:51:16,174 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:502:46: 2025-09-09T00:51:16,174 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:16,174 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:16,174 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:16,174 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]’, 2025-09-09T00:51:16,174 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:16,174 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:16,174 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, 2025-09-09T00:51:16,175 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:504:47: 2025-09-09T00:51:16,175 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:16,175 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:16,175 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:16,740 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadSinglePointCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:51:16,740 ./src/formats/nwchemformat.cpp:758:5: warning: ‘energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:51:16,740 758 | if (energy == 0) 2025-09-09T00:51:16,740 | ^~ 2025-09-09T00:51:16,740 ./src/formats/nwchemformat.cpp:736:12: note: ‘energy’ was declared here 2025-09-09T00:51:16,740 736 | double energy; 2025-09-09T00:51:16,741 | ^~~~~~ 2025-09-09T00:51:18,847 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/nwchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:18,847 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/nwchemformat.o /tmp/ccUitTIZ.s 2025-09-09T00:51:18,852 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:19,777 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:19,778 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:19,778 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/nwchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/nwchemformat.' 2025-09-09T00:51:19,781 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/opendxformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/opendxformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:19,785 Using built-in specs. 2025-09-09T00:51:19,786 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:19,786 Target: arm-linux-gnueabihf 2025-09-09T00:51:19,786 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:19,786 Thread model: posix 2025-09-09T00:51:19,786 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:19,786 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:19,787 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/opendxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:19,787 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/opendxformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase opendxformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc69OG2T.s 2025-09-09T00:51:19,797 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:19,797 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:19,797 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:19,797 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:19,797 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:19,797 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:19,798 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:19,798 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:19,798 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:19,798 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:19,798 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:19,798 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:19,798 #include "..." search starts here: 2025-09-09T00:51:19,798 #include <...> search starts here: 2025-09-09T00:51:19,798 /usr/include/eigen3 2025-09-09T00:51:19,799 include 2025-09-09T00:51:19,799 /usr/include/python3.13 2025-09-09T00:51:19,799 /usr/include/c++/14 2025-09-09T00:51:19,799 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:19,799 /usr/include/c++/14/backward 2025-09-09T00:51:19,799 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:19,799 /usr/local/include 2025-09-09T00:51:19,799 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:19,799 /usr/include 2025-09-09T00:51:19,799 End of search list. 2025-09-09T00:51:19,814 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:21,311 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:21,312 from include/openbabel/mol.h:43, 2025-09-09T00:51:21,312 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:21,312 from ./src/formats/opendxformat.cpp:24: 2025-09-09T00:51:21,312 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:21,312 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:21,312 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:21,312 | ^ 2025-09-09T00:51:21,312 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:21,312 37 | # define UNUSED(x) x 2025-09-09T00:51:21,313 | ^ 2025-09-09T00:51:21,924 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:21,925 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:21,925 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:21,925 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:21,925 | ^ 2025-09-09T00:51:21,925 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:21,925 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:21,925 | ^~~~~~~~ 2025-09-09T00:51:21,928 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:21,929 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:21,929 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:21,929 | ^ 2025-09-09T00:51:21,929 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:21,929 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:21,929 | ^~~~~~~~ 2025-09-09T00:51:21,943 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:21,943 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:21,943 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:21,943 | ^ 2025-09-09T00:51:21,943 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:21,943 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:21,944 | ^~~~~~~~ 2025-09-09T00:51:21,948 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:21,948 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:21,948 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:21,948 | ^ 2025-09-09T00:51:21,948 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:21,948 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:21,949 | ^~~~~~~~ 2025-09-09T00:51:22,087 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:22,087 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:22,087 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:22,087 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:22,087 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:22,087 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:22,087 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:22,088 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:51:22,088 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:51:22,088 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:51:22,088 from /usr/include/c++/14/ios:44, 2025-09-09T00:51:22,088 from /usr/include/c++/14/istream:40, 2025-09-09T00:51:22,088 from /usr/include/c++/14/sstream:40, 2025-09-09T00:51:22,088 from ./src/formats/opendxformat.cpp:21: 2025-09-09T00:51:22,088 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:22,088 131 | struct binary_function 2025-09-09T00:51:22,088 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:22,248 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:51:22,249 229 | virtual const std::string &GetValue() const 2025-09-09T00:51:22,249 | ^~~~~~~~ 2025-09-09T00:51:22,249 In file included from ./src/formats/opendxformat.cpp:25: 2025-09-09T00:51:22,249 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:51:22,249 76 | double GetValue (vector3 pos) const; 2025-09-09T00:51:22,249 | ^~~~~~~~ 2025-09-09T00:51:22,251 ./src/formats/opendxformat.cpp: In member function ‘virtual int OpenBabel::OBOpenDXCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:51:22,251 ./src/formats/opendxformat.cpp:65:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:51:22,251 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:51:22,251 | ~~~~^ 2025-09-09T00:51:22,251 ./src/formats/opendxformat.cpp:65:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:51:22,251 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:51:22,252 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:51:25,560 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/opendxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:25,561 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/opendxformat.o /tmp/cc69OG2T.s 2025-09-09T00:51:25,568 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:25,852 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:25,852 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:25,853 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/opendxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/opendxformat.' 2025-09-09T00:51:25,855 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/orcaformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/orcaformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:25,858 Using built-in specs. 2025-09-09T00:51:25,859 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:25,859 Target: arm-linux-gnueabihf 2025-09-09T00:51:25,859 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:25,859 Thread model: posix 2025-09-09T00:51:25,860 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:25,860 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:25,860 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/orcaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:25,860 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/orcaformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase orcaformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccnemJya.s 2025-09-09T00:51:25,869 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:25,870 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:25,870 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:25,870 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:25,871 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:25,880 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:25,880 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:25,880 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:25,880 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:25,880 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:25,881 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:25,881 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:25,881 #include "..." search starts here: 2025-09-09T00:51:25,881 #include <...> search starts here: 2025-09-09T00:51:25,881 /usr/include/eigen3 2025-09-09T00:51:25,881 include 2025-09-09T00:51:25,881 /usr/include/python3.13 2025-09-09T00:51:25,882 /usr/include/c++/14 2025-09-09T00:51:25,882 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:25,882 /usr/include/c++/14/backward 2025-09-09T00:51:25,882 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:25,882 /usr/local/include 2025-09-09T00:51:25,882 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:25,882 /usr/include 2025-09-09T00:51:25,882 End of search list. 2025-09-09T00:51:25,900 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:27,412 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:27,412 from include/openbabel/mol.h:43, 2025-09-09T00:51:27,412 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:27,412 from ./src/formats/orcaformat.cpp:18: 2025-09-09T00:51:27,412 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:27,413 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:27,413 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:27,413 | ^ 2025-09-09T00:51:27,413 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:27,413 37 | # define UNUSED(x) x 2025-09-09T00:51:27,413 | ^ 2025-09-09T00:51:28,025 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:28,025 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:28,026 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:28,026 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:28,026 | ^ 2025-09-09T00:51:28,026 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:28,026 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:28,026 | ^~~~~~~~ 2025-09-09T00:51:28,030 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:28,030 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:28,031 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:28,031 | ^ 2025-09-09T00:51:28,031 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:28,031 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:28,031 | ^~~~~~~~ 2025-09-09T00:51:28,046 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:28,046 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:28,046 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:28,046 | ^ 2025-09-09T00:51:28,046 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:28,046 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:28,046 | ^~~~~~~~ 2025-09-09T00:51:28,051 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:28,052 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:28,052 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:28,052 | ^ 2025-09-09T00:51:28,052 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:28,052 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:28,052 | ^~~~~~~~ 2025-09-09T00:51:28,191 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:28,191 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:28,191 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:28,191 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:28,191 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:28,191 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:28,192 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:28,192 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:28,193 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:28,193 from include/openbabel/mol.h:35: 2025-09-09T00:51:28,193 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:28,193 131 | struct binary_function 2025-09-09T00:51:28,193 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:28,530 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:51:28,530 ./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] 2025-09-09T00:51:28,530 338 | while(vs.size() == nColumn+1) { 2025-09-09T00:51:28,530 | ~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T00:51:28,532 ./src/formats/orcaformat.cpp:353:48: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:51:28,532 353 | for (unsigned int i = 0; i < nColumn; i++) { 2025-09-09T00:51:28,532 | ~~^~~~~~~~~ 2025-09-09T00:51:28,534 ./src/formats/orcaformat.cpp:365:44: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:51:28,534 365 | for (unsigned int i = 0; i < nColumn; i++) { 2025-09-09T00:51:28,534 | ~~^~~~~~~~~ 2025-09-09T00:51:28,546 ./src/formats/orcaformat.cpp:121:12: warning: unused variable ‘energy’ [-Wunused-variable] 2025-09-09T00:51:28,547 121 | double energy=0; 2025-09-09T00:51:28,547 | ^~~~~~ 2025-09-09T00:51:28,547 ./src/formats/orcaformat.cpp:128:9: warning: variable ‘nModeAll’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:51:28,547 128 | int nModeAll = 0; 2025-09-09T00:51:28,547 | ^~~~~~~~ 2025-09-09T00:51:28,564 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:51:28,565 ./src/formats/orcaformat.cpp:646:10: warning: unused variable ‘buffer’ [-Wunused-variable] 2025-09-09T00:51:28,565 646 | char buffer[BUFF_SIZE]; 2025-09-09T00:51:28,565 | ^~~~~~ 2025-09-09T00:51:32,766 In file included from /usr/include/c++/14/vector:65: 2025-09-09T00:51:32,766 /usr/include/c++/14/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’: 2025-09-09T00:51:32,766 /usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:32,766 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2025-09-09T00:51:32,766 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:51:32,767 /usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:32,803 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]’, 2025-09-09T00:51:32,803 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:32,803 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:32,803 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31: 2025-09-09T00:51:32,804 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:32,804 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:32,804 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:32,894 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]’, 2025-09-09T00:51:32,894 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:32,894 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:32,894 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++/14/bits/stl_vector.h:1624:35, 2025-09-09T00:51:32,895 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++/14/bits/vector.tcc:238:44: 2025-09-09T00:51:32,895 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:32,895 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:32,895 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:34,685 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:51:34,685 ./src/formats/orcaformat.cpp:139:13: warning: ‘confCoords’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:51:34,685 139 | double* confCoords; 2025-09-09T00:51:34,685 | ^~~~~~~~~~ 2025-09-09T00:51:34,686 ./src/formats/orcaformat.cpp:210:36: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:51:34,686 210 | atom->SetVector(x,y,z); //set atom coordinates 2025-09-09T00:51:34,686 | ~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:51:34,686 ./src/formats/orcaformat.cpp:152:13: note: ‘atom’ was declared here 2025-09-09T00:51:34,686 152 | OBAtom *atom; 2025-09-09T00:51:34,686 | ^~~~ 2025-09-09T00:51:39,076 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]’, 2025-09-09T00:51:39,076 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:39,076 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:39,076 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, 2025-09-09T00:51:39,076 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:51:39,076 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:51:39,077 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:39,077 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:39,077 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:39,078 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]’, 2025-09-09T00:51:39,078 inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = OpenBabel::OBOrbital*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, 2025-09-09T00:51:39,078 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++/14/bits/stl_uninitialized.h:373:37, 2025-09-09T00:51:39,078 inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = OpenBabel::OBOrbital; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, 2025-09-09T00:51:39,078 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:51:39,078 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:51:39,078 /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T00:51:39,078 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:51:39,078 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:39,407 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/orcaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:39,408 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/orcaformat.o /tmp/ccnemJya.s 2025-09-09T00:51:39,413 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:40,270 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:40,270 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:40,270 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/orcaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/orcaformat.' 2025-09-09T00:51:40,274 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/outformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/outformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:40,278 Using built-in specs. 2025-09-09T00:51:40,280 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:40,280 Target: arm-linux-gnueabihf 2025-09-09T00:51:40,280 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:40,280 Thread model: posix 2025-09-09T00:51:40,281 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:40,281 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:40,281 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/outformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:40,283 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/outformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase outformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cce5BOSm.s 2025-09-09T00:51:40,295 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:40,295 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:40,296 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:40,296 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:40,296 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:40,297 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:40,297 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:40,297 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:40,297 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:40,298 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:40,298 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:40,298 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:40,298 #include "..." search starts here: 2025-09-09T00:51:40,299 #include <...> search starts here: 2025-09-09T00:51:40,299 /usr/include/eigen3 2025-09-09T00:51:40,299 include 2025-09-09T00:51:40,299 /usr/include/python3.13 2025-09-09T00:51:40,299 /usr/include/c++/14 2025-09-09T00:51:40,299 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:40,300 /usr/include/c++/14/backward 2025-09-09T00:51:40,300 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:40,300 /usr/local/include 2025-09-09T00:51:40,300 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:40,300 /usr/include 2025-09-09T00:51:40,301 End of search list. 2025-09-09T00:51:40,322 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:41,843 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:41,843 from include/openbabel/mol.h:43, 2025-09-09T00:51:41,843 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:41,843 from ./src/formats/outformat.cpp:16: 2025-09-09T00:51:41,844 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:41,844 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:41,844 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:41,844 | ^ 2025-09-09T00:51:41,844 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:41,844 37 | # define UNUSED(x) x 2025-09-09T00:51:41,844 | ^ 2025-09-09T00:51:42,458 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:42,458 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:42,458 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:42,458 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:42,458 | ^ 2025-09-09T00:51:42,459 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:42,459 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:42,459 | ^~~~~~~~ 2025-09-09T00:51:42,463 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:42,463 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:42,463 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:42,463 | ^ 2025-09-09T00:51:42,463 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:42,464 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:42,464 | ^~~~~~~~ 2025-09-09T00:51:42,478 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:42,478 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:42,478 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:42,479 | ^ 2025-09-09T00:51:42,479 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:42,479 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:42,479 | ^~~~~~~~ 2025-09-09T00:51:42,484 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:42,484 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:42,484 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:42,485 | ^ 2025-09-09T00:51:42,485 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:42,485 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:42,485 | ^~~~~~~~ 2025-09-09T00:51:42,624 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:42,625 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:42,625 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:42,625 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:42,625 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:42,625 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:42,625 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:42,626 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:42,626 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:42,626 from include/openbabel/mol.h:35: 2025-09-09T00:51:42,626 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:42,626 131 | struct binary_function 2025-09-09T00:51:42,626 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:44,909 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/outformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:44,910 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/outformat.o /tmp/cce5BOSm.s 2025-09-09T00:51:44,916 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:45,103 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:45,103 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:45,103 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/outformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/outformat.' 2025-09-09T00:51:45,105 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/painterformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/painterformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:45,109 Using built-in specs. 2025-09-09T00:51:45,110 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:45,110 Target: arm-linux-gnueabihf 2025-09-09T00:51:45,110 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:45,110 Thread model: posix 2025-09-09T00:51:45,110 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:45,110 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:45,111 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/painterformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:45,111 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/painterformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase painterformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc4Lhdpr.s 2025-09-09T00:51:45,121 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:45,122 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:45,122 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:45,122 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:45,123 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:45,123 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:45,123 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:45,123 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:45,123 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:45,123 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:45,123 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:45,124 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:45,124 #include "..." search starts here: 2025-09-09T00:51:45,124 #include <...> search starts here: 2025-09-09T00:51:45,124 /usr/include/eigen3 2025-09-09T00:51:45,124 include 2025-09-09T00:51:45,124 /usr/include/python3.13 2025-09-09T00:51:45,124 /usr/include/c++/14 2025-09-09T00:51:45,124 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:45,124 /usr/include/c++/14/backward 2025-09-09T00:51:45,124 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:45,125 /usr/local/include 2025-09-09T00:51:45,125 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:45,125 /usr/include 2025-09-09T00:51:45,125 End of search list. 2025-09-09T00:51:45,139 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:46,647 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:46,647 from include/openbabel/mol.h:43, 2025-09-09T00:51:46,647 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:46,648 from ./src/formats/painterformat.cpp:19: 2025-09-09T00:51:46,648 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:46,648 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:46,648 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:46,648 | ^ 2025-09-09T00:51:46,648 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:46,648 37 | # define UNUSED(x) x 2025-09-09T00:51:46,648 | ^ 2025-09-09T00:51:47,259 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:47,260 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:47,260 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:47,260 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:47,260 | ^ 2025-09-09T00:51:47,260 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:47,260 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:47,260 | ^~~~~~~~ 2025-09-09T00:51:47,263 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:47,263 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:47,264 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:47,264 | ^ 2025-09-09T00:51:47,264 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:47,264 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:47,264 | ^~~~~~~~ 2025-09-09T00:51:47,278 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:47,278 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:47,278 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:47,278 | ^ 2025-09-09T00:51:47,278 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:47,278 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:47,278 | ^~~~~~~~ 2025-09-09T00:51:47,283 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:47,283 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:47,283 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:47,283 | ^ 2025-09-09T00:51:47,283 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:47,283 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:47,283 | ^~~~~~~~ 2025-09-09T00:51:47,421 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:47,422 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:47,422 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:47,422 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:47,422 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:47,422 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:47,422 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:47,422 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:47,422 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:47,422 from include/openbabel/mol.h:35: 2025-09-09T00:51:47,423 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:47,423 131 | struct binary_function 2025-09-09T00:51:47,423 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:47,610 In file included from ./src/formats/painterformat.cpp:22: 2025-09-09T00:51:47,610 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:51:47,610 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:51:47,610 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2025-09-09T00:51:47,610 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:51:47,610 ./src/formats/painterformat.cpp: In member function ‘virtual bool OpenBabel::PainterFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:51:47,610 ./src/formats/painterformat.cpp:113:12: warning: unused variable ‘ofs’ [-Wunused-variable] 2025-09-09T00:51:47,610 113 | ostream& ofs = *pConv->GetOutStream(); 2025-09-09T00:51:47,611 | ^~~ 2025-09-09T00:51:49,573 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/painterformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:49,573 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/painterformat.o /tmp/cc4Lhdpr.s 2025-09-09T00:51:49,580 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:49,767 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:49,768 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:49,768 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/painterformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/painterformat.' 2025-09-09T00:51:49,768 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/pcmodelformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/pcmodelformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:49,773 Using built-in specs. 2025-09-09T00:51:49,774 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:49,774 Target: arm-linux-gnueabihf 2025-09-09T00:51:49,774 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:49,774 Thread model: posix 2025-09-09T00:51:49,774 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:49,774 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:49,774 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pcmodelformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:49,774 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pcmodelformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase pcmodelformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccy61vc0.s 2025-09-09T00:51:49,790 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:49,790 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:49,790 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:49,790 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:49,790 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:49,790 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:49,791 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:49,791 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:49,791 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:49,791 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:49,791 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:49,791 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:49,791 #include "..." search starts here: 2025-09-09T00:51:49,791 #include <...> search starts here: 2025-09-09T00:51:49,792 /usr/include/eigen3 2025-09-09T00:51:49,792 include 2025-09-09T00:51:49,792 /usr/include/python3.13 2025-09-09T00:51:49,792 /usr/include/c++/14 2025-09-09T00:51:49,792 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:49,792 /usr/include/c++/14/backward 2025-09-09T00:51:49,792 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:49,792 /usr/local/include 2025-09-09T00:51:49,793 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:49,793 /usr/include 2025-09-09T00:51:49,793 End of search list. 2025-09-09T00:51:49,805 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:51,306 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:51,306 from include/openbabel/mol.h:43, 2025-09-09T00:51:51,306 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:51,307 from ./src/formats/pcmodelformat.cpp:16: 2025-09-09T00:51:51,307 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:51,307 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:51,307 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:51,307 | ^ 2025-09-09T00:51:51,307 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:51,307 37 | # define UNUSED(x) x 2025-09-09T00:51:51,307 | ^ 2025-09-09T00:51:51,920 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:51,920 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:51,920 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:51,920 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:51,920 | ^ 2025-09-09T00:51:51,920 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:51,920 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:51,920 | ^~~~~~~~ 2025-09-09T00:51:51,921 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:51,921 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:51,921 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:51,921 | ^ 2025-09-09T00:51:51,921 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:51,921 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:51,921 | ^~~~~~~~ 2025-09-09T00:51:51,940 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:51,940 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:51,940 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:51,940 | ^ 2025-09-09T00:51:51,940 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:51,940 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:51,940 | ^~~~~~~~ 2025-09-09T00:51:51,940 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:51,941 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:51,941 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:51,941 | ^ 2025-09-09T00:51:51,941 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:51,941 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:51,941 | ^~~~~~~~ 2025-09-09T00:51:52,078 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:52,078 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:52,078 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:52,078 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:52,078 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:52,078 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:52,078 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:52,080 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:52,080 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:52,080 from include/openbabel/mol.h:35: 2025-09-09T00:51:52,080 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:52,080 131 | struct binary_function 2025-09-09T00:51:52,080 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:54,812 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pcmodelformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:54,813 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/pcmodelformat.o /tmp/ccy61vc0.s 2025-09-09T00:51:54,818 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:55,051 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:51:55,051 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:51:55,051 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pcmodelformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/pcmodelformat.' 2025-09-09T00:51:55,052 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/pdbformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/pdbformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:51:55,056 Using built-in specs. 2025-09-09T00:51:55,057 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:55,057 Target: arm-linux-gnueabihf 2025-09-09T00:51:55,057 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:51:55,057 Thread model: posix 2025-09-09T00:51:55,057 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:55,057 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:55,057 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:51:55,057 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pdbformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase pdbformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccdaa333.s 2025-09-09T00:51:55,070 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:55,070 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:51:55,070 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:55,070 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:55,070 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:55,070 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:55,070 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:55,070 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:55,071 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:55,071 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:55,071 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:55,071 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:55,071 #include "..." search starts here: 2025-09-09T00:51:55,071 #include <...> search starts here: 2025-09-09T00:51:55,071 /usr/include/eigen3 2025-09-09T00:51:55,071 include 2025-09-09T00:51:55,071 /usr/include/python3.13 2025-09-09T00:51:55,072 /usr/include/c++/14 2025-09-09T00:51:55,072 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:55,072 /usr/include/c++/14/backward 2025-09-09T00:51:55,072 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:55,072 /usr/local/include 2025-09-09T00:51:55,072 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:55,072 /usr/include 2025-09-09T00:51:55,072 End of search list. 2025-09-09T00:51:55,090 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:56,590 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:56,590 from include/openbabel/mol.h:43, 2025-09-09T00:51:56,590 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:56,590 from ./src/formats/pdbformat.cpp:17: 2025-09-09T00:51:56,590 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:56,590 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:56,590 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:56,590 | ^ 2025-09-09T00:51:56,590 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:56,591 37 | # define UNUSED(x) x 2025-09-09T00:51:56,591 | ^ 2025-09-09T00:51:57,195 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:57,195 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:57,195 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:57,195 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:57,195 | ^ 2025-09-09T00:51:57,195 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:57,196 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:57,196 | ^~~~~~~~ 2025-09-09T00:51:57,200 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:57,200 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:57,200 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:57,200 | ^ 2025-09-09T00:51:57,200 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:57,200 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:57,200 | ^~~~~~~~ 2025-09-09T00:51:57,215 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:57,215 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:57,215 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:57,215 | ^ 2025-09-09T00:51:57,216 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:57,216 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:57,216 | ^~~~~~~~ 2025-09-09T00:51:57,221 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:57,221 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:57,221 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:57,222 | ^ 2025-09-09T00:51:57,222 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:57,222 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:57,222 | ^~~~~~~~ 2025-09-09T00:51:57,361 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:57,361 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:57,361 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:57,361 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:57,361 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:57,361 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:57,361 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:57,362 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:57,362 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:57,362 from include/openbabel/mol.h:35: 2025-09-09T00:51:57,362 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:57,362 131 | struct binary_function 2025-09-09T00:51:57,363 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:00,572 ./src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:00,572 ./src/formats/pdbformat.cpp:623:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:52:00,572 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:52:00,572 | ^ 2025-09-09T00:52:00,573 ./src/formats/pdbformat.cpp:623:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:52:00,573 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:52:00,573 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:00,573 ./src/formats/pdbformat.cpp:641:70: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:52:00,573 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:52:00,574 | ^ 2025-09-09T00:52:00,574 ./src/formats/pdbformat.cpp:641:29: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:52:00,574 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:52:00,574 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:00,574 ./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=] 2025-09-09T00:52:00,574 678 | snprintf(scharge, 3, "%+d", charge); 2025-09-09T00:52:00,575 | ^~~ 2025-09-09T00:52:00,575 ./src/formats/pdbformat.cpp:678:34: note: directive argument in the range [-32768, 32767] 2025-09-09T00:52:00,575 678 | snprintf(scharge, 3, "%+d", charge); 2025-09-09T00:52:00,575 | ^~~~~ 2025-09-09T00:52:00,575 ./src/formats/pdbformat.cpp:678:21: note: ‘snprintf’ output between 3 and 7 bytes into a destination of size 3 2025-09-09T00:52:00,575 678 | snprintf(scharge, 3, "%+d", charge); 2025-09-09T00:52:00,575 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:03,708 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:52:03,708 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:347:34, 2025-09-09T00:52:03,708 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:52:03,708 ./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] 2025-09-09T00:52:03,709 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:52:03,709 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:03,709 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:52:03,710 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:404:66, 2025-09-09T00:52:03,710 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:52:03,710 ./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] 2025-09-09T00:52:03,710 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:52:03,710 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:03,710 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:52:03,711 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:407:66, 2025-09-09T00:52:03,711 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:52:03,711 ./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] 2025-09-09T00:52:03,711 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:52:03,711 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:03,711 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:52:03,711 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:408:66, 2025-09-09T00:52:03,711 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:52:03,711 ./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] 2025-09-09T00:52:03,712 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:52:03,712 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:03,712 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:52:03,712 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:409:66, 2025-09-09T00:52:03,712 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:52:03,712 ./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] 2025-09-09T00:52:03,712 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:52:03,712 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:05,515 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:05,516 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/pdbformat.o /tmp/ccdaa333.s 2025-09-09T00:52:05,521 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:06,247 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:52:06,248 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:52:06,248 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbformat.' 2025-09-09T00:52:06,251 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/pdbqtformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/pdbqtformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:52:06,255 Using built-in specs. 2025-09-09T00:52:06,257 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:06,257 Target: arm-linux-gnueabihf 2025-09-09T00:52:06,257 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:52:06,257 Thread model: posix 2025-09-09T00:52:06,257 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:06,258 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:06,258 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbqtformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:06,260 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pdbqtformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase pdbqtformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccRHgjr6.s 2025-09-09T00:52:06,270 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:06,271 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:52:06,271 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:06,271 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:06,272 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:06,273 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:06,273 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:06,273 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:06,273 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:06,274 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:06,274 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:06,274 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:06,274 #include "..." search starts here: 2025-09-09T00:52:06,275 #include <...> search starts here: 2025-09-09T00:52:06,275 /usr/include/eigen3 2025-09-09T00:52:06,275 include 2025-09-09T00:52:06,275 /usr/include/python3.13 2025-09-09T00:52:06,275 /usr/include/c++/14 2025-09-09T00:52:06,276 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:06,276 /usr/include/c++/14/backward 2025-09-09T00:52:06,276 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:06,276 /usr/local/include 2025-09-09T00:52:06,276 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:06,277 /usr/include 2025-09-09T00:52:06,277 End of search list. 2025-09-09T00:52:06,297 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:07,804 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:07,804 from include/openbabel/mol.h:43, 2025-09-09T00:52:07,804 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:07,804 from ./src/formats/pdbqtformat.cpp:24: 2025-09-09T00:52:07,804 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:07,804 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:07,804 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:07,805 | ^ 2025-09-09T00:52:07,805 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:07,805 37 | # define UNUSED(x) x 2025-09-09T00:52:07,805 | ^ 2025-09-09T00:52:08,416 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:08,416 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:08,416 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:08,416 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:08,416 | ^ 2025-09-09T00:52:08,417 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:08,417 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:08,417 | ^~~~~~~~ 2025-09-09T00:52:08,421 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:08,421 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:08,421 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:08,421 | ^ 2025-09-09T00:52:08,422 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:08,422 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:08,422 | ^~~~~~~~ 2025-09-09T00:52:08,436 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:08,436 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:08,437 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:08,437 | ^ 2025-09-09T00:52:08,437 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:08,437 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:08,437 | ^~~~~~~~ 2025-09-09T00:52:08,442 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:08,442 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:08,443 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:08,443 | ^ 2025-09-09T00:52:08,443 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:08,443 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:08,443 | ^~~~~~~~ 2025-09-09T00:52:08,581 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:08,582 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:08,582 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:08,582 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:08,582 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:08,582 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:08,582 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:08,583 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:08,583 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:08,583 from include/openbabel/mol.h:35: 2025-09-09T00:52:08,583 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:08,583 131 | struct binary_function 2025-09-09T00:52:08,583 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:08,889 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::OutputTree(OBConversion*, OBMol&, std::ostream&, std::map&, unsigned int, bool, bool)’: 2025-09-09T00:52:08,890 ./src/formats/pdbqtformat.cpp:580:20: warning: unused variable ‘child’ [-Wunused-variable] 2025-09-09T00:52:08,890 580 | unsigned int child=i; 2025-09-09T00:52:08,890 | ^~~~~ 2025-09-09T00:52:08,926 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::ConstructTree(std::map&, std::vector >, unsigned int, const OBMol&, bool)’: 2025-09-09T00:52:08,926 ./src/formats/pdbqtformat.cpp:609:145: warning: unused parameter ‘flexible’ [-Wunused-parameter] 2025-09-09T00:52:08,926 609 | void ConstructTree (map & tree, vector > rigid_fragments, unsigned int root_piece, const OBMol& mol, bool flexible) 2025-09-09T00:52:08,926 | ~~~~~^~~~~~~~ 2025-09-09T00:52:08,942 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::Separate_preserve_charges(OBMol&, std::vector&)’: 2025-09-09T00:52:08,942 ./src/formats/pdbqtformat.cpp:794:9: warning: unused variable ‘fragments’ [-Wunused-variable] 2025-09-09T00:52:08,942 794 | int fragments = 0; 2025-09-09T00:52:08,942 | ^~~~~~~~~ 2025-09-09T00:52:09,008 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::parseAtomRecord(char*, OBMol&, int)’: 2025-09-09T00:52:09,008 ./src/formats/pdbqtformat.cpp:1045:60: warning: unused parameter ‘chainNum’ [-Wunused-parameter] 2025-09-09T00:52:09,008 1045 | static bool parseAtomRecord(char *buffer, OBMol &mol,int chainNum) 2025-09-09T00:52:09,008 | ~~~~^~~~~~~~ 2025-09-09T00:52:10,338 ./src/formats/pdbqtformat.cpp: At global scope: 2025-09-09T00:52:10,339 ./src/formats/pdbqtformat.cpp:747:16: warning: ‘unsigned int OpenBabel::AtomsSoFar(const std::map&, unsigned int)’ defined but not used [-Wunused-function] 2025-09-09T00:52:10,339 747 | unsigned int AtomsSoFar(const map & tree, unsigned int depth) 2025-09-09T00:52:10,339 | ^~~~~~~~~~ 2025-09-09T00:52:12,679 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::OutputAtom(OBAtom*, std::ostream&, unsigned int)’: 2025-09-09T00:52:12,680 ./src/formats/pdbqtformat.cpp:334:52: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:52:12,680 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:52:12,680 | ^ 2025-09-09T00:52:12,680 ./src/formats/pdbqtformat.cpp:334:15: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:52:12,680 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:52:12,680 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:12,681 ./src/formats/pdbqtformat.cpp:351:60: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:52:12,681 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:52:12,681 | ^ 2025-09-09T00:52:12,681 ./src/formats/pdbqtformat.cpp:351:19: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:52:12,681 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:52:12,681 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:19,940 ./src/formats/pdbqtformat.cpp: In member function ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:19,940 ./src/formats/pdbqtformat.cpp:915:22: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 10 equals destination size [-Wstringop-truncation] 2025-09-09T00:52:19,941 915 | strncpy(type_name, etab.GetSymbol(rotBondTable[rotBondId][bondAtomNum]->GetAtomicNum()), sizeof(type_name)); 2025-09-09T00:52:19,941 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:22,033 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbqtformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:22,034 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/pdbqtformat.o /tmp/ccRHgjr6.s 2025-09-09T00:52:22,039 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:23,194 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:52:23,194 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:52:23,194 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbqtformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/pdbqtformat.' 2025-09-09T00:52:23,194 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/pointcloudformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/pointcloudformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:52:23,198 Using built-in specs. 2025-09-09T00:52:23,199 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:23,199 Target: arm-linux-gnueabihf 2025-09-09T00:52:23,200 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:52:23,200 Thread model: posix 2025-09-09T00:52:23,200 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:23,200 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:23,201 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pointcloudformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:23,202 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pointcloudformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase pointcloudformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccMlaUlN.s 2025-09-09T00:52:23,213 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:23,213 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:52:23,214 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:23,214 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:23,215 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:23,215 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:23,216 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:23,216 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:23,216 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:23,216 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:23,217 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:23,217 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:23,217 #include "..." search starts here: 2025-09-09T00:52:23,217 #include <...> search starts here: 2025-09-09T00:52:23,217 /usr/include/eigen3 2025-09-09T00:52:23,218 include 2025-09-09T00:52:23,218 /usr/include/python3.13 2025-09-09T00:52:23,218 /usr/include/c++/14 2025-09-09T00:52:23,218 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:23,218 /usr/include/c++/14/backward 2025-09-09T00:52:23,219 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:23,219 /usr/local/include 2025-09-09T00:52:23,219 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:23,219 /usr/include 2025-09-09T00:52:23,219 End of search list. 2025-09-09T00:52:23,238 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:24,748 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:24,748 from include/openbabel/mol.h:43, 2025-09-09T00:52:24,748 from ./src/formats/pointcloudformat.cpp:28: 2025-09-09T00:52:24,748 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:24,749 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:24,749 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:24,749 | ^ 2025-09-09T00:52:24,749 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:24,749 37 | # define UNUSED(x) x 2025-09-09T00:52:24,749 | ^ 2025-09-09T00:52:25,361 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:25,361 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:25,361 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:25,361 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:25,361 | ^ 2025-09-09T00:52:25,362 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:25,362 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:25,362 | ^~~~~~~~ 2025-09-09T00:52:25,366 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:25,366 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:25,366 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:25,366 | ^ 2025-09-09T00:52:25,366 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:25,366 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:25,366 | ^~~~~~~~ 2025-09-09T00:52:25,381 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:25,381 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:25,381 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:25,381 | ^ 2025-09-09T00:52:25,382 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:25,382 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:25,382 | ^~~~~~~~ 2025-09-09T00:52:25,387 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:25,387 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:25,387 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:25,387 | ^ 2025-09-09T00:52:25,388 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:25,388 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:25,388 | ^~~~~~~~ 2025-09-09T00:52:25,527 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:25,527 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:25,527 from ./src/formats/pointcloudformat.cpp:29: 2025-09-09T00:52:25,527 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:25,527 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:25,527 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:25,527 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:25,528 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:25,528 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:25,528 from include/openbabel/mol.h:35: 2025-09-09T00:52:25,528 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:25,528 131 | struct binary_function 2025-09-09T00:52:25,529 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:25,691 ./src/formats/pointcloudformat.cpp: In member function ‘virtual int OpenBabel::PointCloudFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:52:25,691 ./src/formats/pointcloudformat.cpp:104:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:52:25,691 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:52:25,691 | ~~~~^ 2025-09-09T00:52:25,691 ./src/formats/pointcloudformat.cpp:104:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:52:25,691 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:52:25,692 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:52:25,708 ./src/formats/pointcloudformat.cpp: In member function ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:25,709 ./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] 2025-09-09T00:52:25,709 217 | for( int j = 0; j < radius_mult_list.size(); j++ ) { 2025-09-09T00:52:25,709 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:28,214 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pointcloudformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:28,215 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/pointcloudformat.o /tmp/ccMlaUlN.s 2025-09-09T00:52:28,224 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:28,450 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:52:28,450 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:52:28,450 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pointcloudformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/pointcloudformat.' 2025-09-09T00:52:28,452 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/posformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/posformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:52:28,456 Using built-in specs. 2025-09-09T00:52:28,457 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:28,458 Target: arm-linux-gnueabihf 2025-09-09T00:52:28,458 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:52:28,458 Thread model: posix 2025-09-09T00:52:28,458 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:28,458 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:28,459 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/posformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:28,461 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/posformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase posformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccv0lyBU.s 2025-09-09T00:52:28,471 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:28,471 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:52:28,472 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:28,472 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:28,474 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:28,474 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:28,475 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:28,475 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:28,475 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:28,475 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:28,476 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:28,476 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:28,476 #include "..." search starts here: 2025-09-09T00:52:28,476 #include <...> search starts here: 2025-09-09T00:52:28,476 /usr/include/eigen3 2025-09-09T00:52:28,477 include 2025-09-09T00:52:28,477 /usr/include/python3.13 2025-09-09T00:52:28,477 /usr/include/c++/14 2025-09-09T00:52:28,477 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:28,477 /usr/include/c++/14/backward 2025-09-09T00:52:28,478 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:28,478 /usr/local/include 2025-09-09T00:52:28,478 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:28,478 /usr/include 2025-09-09T00:52:28,478 End of search list. 2025-09-09T00:52:28,498 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:30,007 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:30,007 from include/openbabel/mol.h:43, 2025-09-09T00:52:30,007 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:30,008 from ./src/formats/posformat.cpp:15: 2025-09-09T00:52:30,008 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:30,008 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:30,008 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:30,008 | ^ 2025-09-09T00:52:30,008 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:30,008 37 | # define UNUSED(x) x 2025-09-09T00:52:30,008 | ^ 2025-09-09T00:52:30,622 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:30,623 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:30,623 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:30,623 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:30,623 | ^ 2025-09-09T00:52:30,623 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:30,623 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:30,623 | ^~~~~~~~ 2025-09-09T00:52:30,627 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:30,627 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:30,628 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:30,628 | ^ 2025-09-09T00:52:30,628 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:30,628 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:30,628 | ^~~~~~~~ 2025-09-09T00:52:30,643 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:30,643 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:30,643 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:30,643 | ^ 2025-09-09T00:52:30,643 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:30,643 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:30,643 | ^~~~~~~~ 2025-09-09T00:52:30,649 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:30,649 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:30,649 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:30,649 | ^ 2025-09-09T00:52:30,649 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:30,649 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:30,649 | ^~~~~~~~ 2025-09-09T00:52:30,788 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:30,789 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:30,789 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:30,789 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:30,789 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:30,789 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:30,789 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:30,790 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:30,790 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:30,790 from include/openbabel/mol.h:35: 2025-09-09T00:52:30,790 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:30,790 131 | struct binary_function 2025-09-09T00:52:30,790 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:30,954 ./src/formats/posformat.cpp: In member function ‘virtual bool OpenBabel::POSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:30,955 ./src/formats/posformat.cpp:101:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:52:30,955 101 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2025-09-09T00:52:30,955 | ~^ ~~~~~~~ 2025-09-09T00:52:30,955 | | | 2025-09-09T00:52:30,955 | | unsigned int* 2025-09-09T00:52:30,955 | int* 2025-09-09T00:52:30,955 | %d 2025-09-09T00:52:33,703 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/posformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:33,704 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/posformat.o /tmp/ccv0lyBU.s 2025-09-09T00:52:33,709 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:33,978 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:52:33,979 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:52:33,979 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/posformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/posformat.' 2025-09-09T00:52:33,981 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/povrayformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/povrayformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:52:33,985 Using built-in specs. 2025-09-09T00:52:33,986 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:33,986 Target: arm-linux-gnueabihf 2025-09-09T00:52:33,987 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:52:33,987 Thread model: posix 2025-09-09T00:52:33,987 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:33,987 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:33,988 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/povrayformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:33,989 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/povrayformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase povrayformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccnPlPhs.s 2025-09-09T00:52:34,000 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:34,001 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:52:34,001 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:34,001 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:34,002 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:34,002 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:34,002 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:34,002 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:34,003 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:34,003 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:34,003 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:34,003 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:34,003 #include "..." search starts here: 2025-09-09T00:52:34,003 #include <...> search starts here: 2025-09-09T00:52:34,003 /usr/include/eigen3 2025-09-09T00:52:34,004 include 2025-09-09T00:52:34,004 /usr/include/python3.13 2025-09-09T00:52:34,004 /usr/include/c++/14 2025-09-09T00:52:34,004 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:34,004 /usr/include/c++/14/backward 2025-09-09T00:52:34,004 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:34,004 /usr/local/include 2025-09-09T00:52:34,005 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:34,005 /usr/include 2025-09-09T00:52:34,005 End of search list. 2025-09-09T00:52:34,021 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:35,537 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:35,537 from include/openbabel/mol.h:43, 2025-09-09T00:52:35,537 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:35,538 from ./src/formats/povrayformat.cpp:23: 2025-09-09T00:52:35,538 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:35,538 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:35,538 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:35,538 | ^ 2025-09-09T00:52:35,538 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:35,538 37 | # define UNUSED(x) x 2025-09-09T00:52:35,538 | ^ 2025-09-09T00:52:36,149 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:36,149 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:36,149 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:36,150 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:36,150 | ^ 2025-09-09T00:52:36,150 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:36,150 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:36,150 | ^~~~~~~~ 2025-09-09T00:52:36,154 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:36,154 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:36,154 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:36,154 | ^ 2025-09-09T00:52:36,155 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:36,155 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:36,155 | ^~~~~~~~ 2025-09-09T00:52:36,169 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:36,170 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:36,170 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:36,170 | ^ 2025-09-09T00:52:36,170 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:36,170 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:36,170 | ^~~~~~~~ 2025-09-09T00:52:36,175 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:36,175 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:36,175 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:36,176 | ^ 2025-09-09T00:52:36,176 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:36,176 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:36,176 | ^~~~~~~~ 2025-09-09T00:52:36,315 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:36,315 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:36,315 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:36,315 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:36,315 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:36,315 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:36,315 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:36,316 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:36,316 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:36,316 from include/openbabel/mol.h:35: 2025-09-09T00:52:36,316 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:36,317 131 | struct binary_function 2025-09-09T00:52:36,317 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:36,550 ./src/formats/povrayformat.cpp: In member function ‘void OpenBabel::PovrayFormat::OutputHeader(std::ostream&, OpenBabel::OBMol&, std::string)’: 2025-09-09T00:52:36,550 ./src/formats/povrayformat.cpp:168:12: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:52:36,550 168 | size_t time_res; /* Result of strftime */ 2025-09-09T00:52:36,550 | ^~~~~~~~ 2025-09-09T00:52:36,550 ./src/formats/povrayformat.cpp:164:68: warning: unused parameter ‘prefix’ [-Wunused-parameter] 2025-09-09T00:52:36,550 164 | void PovrayFormat::OutputHeader(ostream &ofs, OBMol &mol, string prefix) 2025-09-09T00:52:36,551 | ~~~~~~~^~~~~~ 2025-09-09T00:52:36,584 ./src/formats/povrayformat.cpp: In function ‘void OpenBabel::OutputCSTBonds(std::ostream&, OBMol&, std::string)’: 2025-09-09T00:52:36,585 ./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] 2025-09-09T00:52:36,585 521 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2025-09-09T00:52:36,585 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:36,585 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:52:36,585 /usr/include/c++/14/backward/binders.h:136:5: note: declared here 2025-09-09T00:52:36,585 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:52:36,585 | ^~~~~~~ 2025-09-09T00:52:36,596 ./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] 2025-09-09T00:52:36,596 582 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2025-09-09T00:52:36,597 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:36,597 /usr/include/c++/14/backward/binders.h:136:5: note: declared here 2025-09-09T00:52:36,597 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:52:36,597 | ^~~~~~~ 2025-09-09T00:52:36,659 ./src/formats/povrayformat.cpp: In member function ‘virtual bool OpenBabel::PovrayFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:36,660 ./src/formats/povrayformat.cpp:802:17: warning: unused variable ‘title’ [-Wunused-variable] 2025-09-09T00:52:36,660 802 | const char* title = pmol->GetTitle(); 2025-09-09T00:52:36,660 | ^~~~~ 2025-09-09T00:52:42,116 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/povrayformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:42,116 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/povrayformat.o /tmp/ccnPlPhs.s 2025-09-09T00:52:42,121 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:42,617 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:52:42,617 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:52:42,618 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/povrayformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/povrayformat.' 2025-09-09T00:52:42,620 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/pqrformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/pqrformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:52:42,624 Using built-in specs. 2025-09-09T00:52:42,624 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:42,625 Target: arm-linux-gnueabihf 2025-09-09T00:52:42,625 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:52:42,625 Thread model: posix 2025-09-09T00:52:42,625 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:42,625 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:42,625 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pqrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:42,625 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pqrformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase pqrformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccwic7LJ.s 2025-09-09T00:52:42,635 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:42,635 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:52:42,635 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:42,635 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:42,635 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:42,636 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:42,636 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:42,636 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:42,636 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:42,636 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:42,636 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:42,636 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:42,636 #include "..." search starts here: 2025-09-09T00:52:42,636 #include <...> search starts here: 2025-09-09T00:52:42,636 /usr/include/eigen3 2025-09-09T00:52:42,637 include 2025-09-09T00:52:42,637 /usr/include/python3.13 2025-09-09T00:52:42,637 /usr/include/c++/14 2025-09-09T00:52:42,637 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:42,637 /usr/include/c++/14/backward 2025-09-09T00:52:42,637 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:42,637 /usr/local/include 2025-09-09T00:52:42,637 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:42,637 /usr/include 2025-09-09T00:52:42,637 End of search list. 2025-09-09T00:52:42,652 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:44,174 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:44,174 from include/openbabel/mol.h:43, 2025-09-09T00:52:44,174 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:44,174 from ./src/formats/pqrformat.cpp:16: 2025-09-09T00:52:44,174 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:44,174 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:44,175 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:44,175 | ^ 2025-09-09T00:52:44,175 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:44,175 37 | # define UNUSED(x) x 2025-09-09T00:52:44,175 | ^ 2025-09-09T00:52:44,787 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:44,787 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:44,787 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:44,787 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:44,787 | ^ 2025-09-09T00:52:44,787 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:44,787 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:44,787 | ^~~~~~~~ 2025-09-09T00:52:44,790 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:44,791 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:44,791 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:44,791 | ^ 2025-09-09T00:52:44,791 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:44,791 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:44,791 | ^~~~~~~~ 2025-09-09T00:52:44,805 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:44,805 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:44,805 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:44,805 | ^ 2025-09-09T00:52:44,805 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:44,806 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:44,806 | ^~~~~~~~ 2025-09-09T00:52:44,810 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:44,810 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:44,810 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:44,810 | ^ 2025-09-09T00:52:44,811 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:44,811 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:44,811 | ^~~~~~~~ 2025-09-09T00:52:44,949 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:44,949 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:44,949 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:44,949 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:44,949 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:44,949 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:44,949 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:44,950 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:44,950 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:44,950 from include/openbabel/mol.h:35: 2025-09-09T00:52:44,950 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:44,950 131 | struct binary_function 2025-09-09T00:52:44,950 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:45,126 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomCharge(char*, OBMol&)’: 2025-09-09T00:52:45,126 ./src/formats/pqrformat.cpp:196:13: warning: unused variable ‘atom’ [-Wunused-variable] 2025-09-09T00:52:45,126 196 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2025-09-09T00:52:45,126 | ^~~~ 2025-09-09T00:52:45,127 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomRadius(char*, OBMol&)’: 2025-09-09T00:52:45,127 ./src/formats/pqrformat.cpp:211:13: warning: unused variable ‘atom’ [-Wunused-variable] 2025-09-09T00:52:45,127 211 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2025-09-09T00:52:45,127 | ^~~~ 2025-09-09T00:52:47,155 ./src/formats/pqrformat.cpp: In member function ‘virtual bool OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:47,155 ./src/formats/pqrformat.cpp:501:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:52:47,155 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:52:47,156 | ^ 2025-09-09T00:52:47,156 ./src/formats/pqrformat.cpp:501:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:52:47,156 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:52:47,156 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:47,156 ./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=] 2025-09-09T00:52:47,156 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:52:47,156 | ^~~~ ~~~ 2025-09-09T00:52:47,156 ./src/formats/pqrformat.cpp:518:29: note: ‘snprintf’ output between 5 and 17 bytes into a destination of size 10 2025-09-09T00:52:47,156 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:52:47,156 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:50,522 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pqrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:50,522 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/pqrformat.o /tmp/ccwic7LJ.s 2025-09-09T00:52:50,527 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:51,050 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:52:51,050 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:52:51,050 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pqrformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/pqrformat.' 2025-09-09T00:52:51,053 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/pwscfformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/pwscfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:52:51,057 Using built-in specs. 2025-09-09T00:52:51,058 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:51,058 Target: arm-linux-gnueabihf 2025-09-09T00:52:51,058 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:52:51,058 Thread model: posix 2025-09-09T00:52:51,059 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:51,059 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:51,059 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pwscfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:51,061 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/pwscfformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase pwscfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cczdhPAF.s 2025-09-09T00:52:51,073 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:51,074 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:52:51,074 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:51,074 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:51,075 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:51,075 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:51,075 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:51,075 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:51,075 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:51,075 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:51,075 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:51,076 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:51,076 #include "..." search starts here: 2025-09-09T00:52:51,076 #include <...> search starts here: 2025-09-09T00:52:51,076 /usr/include/eigen3 2025-09-09T00:52:51,076 include 2025-09-09T00:52:51,076 /usr/include/python3.13 2025-09-09T00:52:51,076 /usr/include/c++/14 2025-09-09T00:52:51,077 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:51,077 /usr/include/c++/14/backward 2025-09-09T00:52:51,077 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:51,077 /usr/local/include 2025-09-09T00:52:51,077 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:51,077 /usr/include 2025-09-09T00:52:51,077 End of search list. 2025-09-09T00:52:51,092 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:52,592 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:52,593 from include/openbabel/mol.h:43, 2025-09-09T00:52:52,593 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:52,593 from ./src/formats/pwscfformat.cpp:16: 2025-09-09T00:52:52,593 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:52,593 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:52,593 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:52,593 | ^ 2025-09-09T00:52:52,593 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:52,594 37 | # define UNUSED(x) x 2025-09-09T00:52:52,594 | ^ 2025-09-09T00:52:53,203 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:53,203 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:53,203 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:53,203 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:53,203 | ^ 2025-09-09T00:52:53,203 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:53,203 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:53,204 | ^~~~~~~~ 2025-09-09T00:52:53,206 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:53,207 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:53,207 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:53,207 | ^ 2025-09-09T00:52:53,207 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:53,207 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:53,207 | ^~~~~~~~ 2025-09-09T00:52:53,221 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:53,221 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:53,221 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:53,221 | ^ 2025-09-09T00:52:53,221 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:53,222 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:53,222 | ^~~~~~~~ 2025-09-09T00:52:53,226 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:53,226 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:53,226 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:53,226 | ^ 2025-09-09T00:52:53,226 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:53,227 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:53,227 | ^~~~~~~~ 2025-09-09T00:52:53,364 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:53,365 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:53,365 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:53,365 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:53,365 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:53,365 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:53,365 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:53,365 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:53,365 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:53,365 from include/openbabel/mol.h:35: 2025-09-09T00:52:53,366 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:53,366 131 | struct binary_function 2025-09-09T00:52:53,366 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:53,527 ./src/formats/pwscfformat.cpp: In member function ‘virtual int OpenBabel::PWscfFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:52:53,527 ./src/formats/pwscfformat.cpp:51:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:52:53,527 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:52:53,527 | ~~~~^ 2025-09-09T00:52:53,528 ./src/formats/pwscfformat.cpp:51:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:52:53,528 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:52:53,528 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:52:55,728 ./src/formats/pwscfformat.cpp: In member function ‘virtual bool OpenBabel::PWscfFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:55,728 ./src/formats/pwscfformat.cpp:274:15: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:52:55,728 274 | snprintf(tag, BUFF_SIZE, "%f", en_kcal_per_mole); 2025-09-09T00:52:55,728 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:55,728 ./src/formats/pwscfformat.cpp:90:12: note: ‘enthalpy’ was declared here 2025-09-09T00:52:55,728 90 | double enthalpy, pv; 2025-09-09T00:52:55,728 | ^~~~~~~~ 2025-09-09T00:52:55,728 ./src/formats/pwscfformat.cpp:273:14: warning: ‘pv’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:52:55,728 273 | double pv_eV = pv / EV_TO_KCAL_PER_MOL; 2025-09-09T00:52:55,729 | ^~~~~ 2025-09-09T00:52:55,729 ./src/formats/pwscfformat.cpp:90:22: note: ‘pv’ was declared here 2025-09-09T00:52:55,729 90 | double enthalpy, pv; 2025-09-09T00:52:55,729 | ^~ 2025-09-09T00:52:56,501 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pwscfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:56,502 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/pwscfformat.o /tmp/cczdhPAF.s 2025-09-09T00:52:56,510 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:56,768 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:52:56,768 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:52:56,768 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/pwscfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/pwscfformat.' 2025-09-09T00:52:56,770 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/qchemformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/qchemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:52:56,774 Using built-in specs. 2025-09-09T00:52:56,775 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:56,775 Target: arm-linux-gnueabihf 2025-09-09T00:52:56,775 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:52:56,775 Thread model: posix 2025-09-09T00:52:56,775 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:56,775 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:56,776 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/qchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:52:56,776 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/qchemformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase qchemformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cccMQah5.s 2025-09-09T00:52:56,787 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:56,787 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:52:56,787 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:56,788 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:56,788 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:56,788 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:56,788 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:56,788 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:56,788 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:56,789 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:56,789 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:56,789 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:56,789 #include "..." search starts here: 2025-09-09T00:52:56,789 #include <...> search starts here: 2025-09-09T00:52:56,789 /usr/include/eigen3 2025-09-09T00:52:56,789 include 2025-09-09T00:52:56,790 /usr/include/python3.13 2025-09-09T00:52:56,790 /usr/include/c++/14 2025-09-09T00:52:56,790 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:56,790 /usr/include/c++/14/backward 2025-09-09T00:52:56,790 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:56,790 /usr/local/include 2025-09-09T00:52:56,790 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:56,790 /usr/include 2025-09-09T00:52:56,791 End of search list. 2025-09-09T00:52:56,806 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:58,300 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:58,300 from include/openbabel/mol.h:43, 2025-09-09T00:52:58,300 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:58,300 from ./src/formats/qchemformat.cpp:17: 2025-09-09T00:52:58,300 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:58,300 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:58,300 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:58,301 | ^ 2025-09-09T00:52:58,301 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:58,301 37 | # define UNUSED(x) x 2025-09-09T00:52:58,301 | ^ 2025-09-09T00:52:58,911 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:58,912 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:58,912 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:58,912 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:58,912 | ^ 2025-09-09T00:52:58,912 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:58,912 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:58,912 | ^~~~~~~~ 2025-09-09T00:52:58,915 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:58,916 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:58,916 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:58,916 | ^ 2025-09-09T00:52:58,916 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:58,916 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:58,916 | ^~~~~~~~ 2025-09-09T00:52:58,930 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:58,930 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:58,930 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:58,930 | ^ 2025-09-09T00:52:58,930 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:58,930 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:58,931 | ^~~~~~~~ 2025-09-09T00:52:58,935 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:58,935 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:58,935 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:58,935 | ^ 2025-09-09T00:52:58,935 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:58,935 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:58,936 | ^~~~~~~~ 2025-09-09T00:52:59,073 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:59,073 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:59,074 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:59,074 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:59,074 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:59,074 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:59,074 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:59,074 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:59,074 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:59,074 from include/openbabel/mol.h:35: 2025-09-09T00:52:59,074 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:59,074 131 | struct binary_function 2025-09-09T00:52:59,075 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:04,091 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/qchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:04,091 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/qchemformat.o /tmp/cccMQah5.s 2025-09-09T00:53:04,096 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:04,550 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:04,550 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:04,550 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/qchemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/qchemformat.' 2025-09-09T00:53:04,552 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/reportformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/reportformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:04,557 Using built-in specs. 2025-09-09T00:53:04,558 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:04,558 Target: arm-linux-gnueabihf 2025-09-09T00:53:04,558 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:04,558 Thread model: posix 2025-09-09T00:53:04,558 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:04,558 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:04,558 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/reportformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:04,558 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/reportformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase reportformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccFYnoG6.s 2025-09-09T00:53:04,568 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:04,568 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:04,568 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:04,568 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:04,569 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:04,569 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:04,569 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:04,569 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:04,569 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:04,569 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:04,569 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:04,569 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:04,569 #include "..." search starts here: 2025-09-09T00:53:04,569 #include <...> search starts here: 2025-09-09T00:53:04,569 /usr/include/eigen3 2025-09-09T00:53:04,570 include 2025-09-09T00:53:04,570 /usr/include/python3.13 2025-09-09T00:53:04,570 /usr/include/c++/14 2025-09-09T00:53:04,570 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:04,570 /usr/include/c++/14/backward 2025-09-09T00:53:04,570 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:04,570 /usr/local/include 2025-09-09T00:53:04,570 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:04,570 /usr/include 2025-09-09T00:53:04,570 End of search list. 2025-09-09T00:53:04,590 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:06,100 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:06,100 from include/openbabel/mol.h:43, 2025-09-09T00:53:06,100 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:06,100 from ./src/formats/reportformat.cpp:23: 2025-09-09T00:53:06,100 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:06,100 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:06,100 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:06,100 | ^ 2025-09-09T00:53:06,100 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:06,101 37 | # define UNUSED(x) x 2025-09-09T00:53:06,101 | ^ 2025-09-09T00:53:06,706 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:06,706 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:06,706 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:06,706 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:06,707 | ^ 2025-09-09T00:53:06,707 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:06,707 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:06,707 | ^~~~~~~~ 2025-09-09T00:53:06,711 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:06,711 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:06,711 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:06,711 | ^ 2025-09-09T00:53:06,712 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:06,712 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:06,712 | ^~~~~~~~ 2025-09-09T00:53:06,726 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:06,727 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:06,727 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:06,727 | ^ 2025-09-09T00:53:06,727 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:06,727 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:06,727 | ^~~~~~~~ 2025-09-09T00:53:06,732 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:06,733 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:06,733 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:06,733 | ^ 2025-09-09T00:53:06,733 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:06,733 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:06,733 | ^~~~~~~~ 2025-09-09T00:53:06,872 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:06,872 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:06,872 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:06,872 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:06,872 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:06,873 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:06,873 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:06,873 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:06,874 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:06,874 from include/openbabel/mol.h:35: 2025-09-09T00:53:06,874 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:06,874 131 | struct binary_function 2025-09-09T00:53:06,874 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:09,434 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/reportformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:09,434 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/reportformat.o /tmp/ccFYnoG6.s 2025-09-09T00:53:09,439 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:09,660 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:09,660 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:09,660 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/reportformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/reportformat.' 2025-09-09T00:53:09,661 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/rsmiformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/rsmiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:09,665 Using built-in specs. 2025-09-09T00:53:09,666 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:09,667 Target: arm-linux-gnueabihf 2025-09-09T00:53:09,667 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:09,667 Thread model: posix 2025-09-09T00:53:09,667 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:09,667 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:09,668 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/rsmiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:09,670 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/rsmiformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase rsmiformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccn0yvvh.s 2025-09-09T00:53:09,680 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:09,680 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:09,680 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:09,680 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:09,680 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:09,680 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:09,680 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:09,681 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:09,681 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:09,681 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:09,681 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:09,681 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:09,681 #include "..." search starts here: 2025-09-09T00:53:09,681 #include <...> search starts here: 2025-09-09T00:53:09,681 /usr/include/eigen3 2025-09-09T00:53:09,682 include 2025-09-09T00:53:09,682 /usr/include/python3.13 2025-09-09T00:53:09,682 /usr/include/c++/14 2025-09-09T00:53:09,682 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:09,682 /usr/include/c++/14/backward 2025-09-09T00:53:09,682 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:09,682 /usr/local/include 2025-09-09T00:53:09,682 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:09,683 /usr/include 2025-09-09T00:53:09,683 End of search list. 2025-09-09T00:53:09,701 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:11,305 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:11,306 from include/openbabel/mol.h:43, 2025-09-09T00:53:11,306 from ./src/formats/rsmiformat.cpp:19: 2025-09-09T00:53:11,306 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:11,306 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:11,306 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:11,306 | ^ 2025-09-09T00:53:11,306 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:11,306 37 | # define UNUSED(x) x 2025-09-09T00:53:11,306 | ^ 2025-09-09T00:53:11,920 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:11,920 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:11,920 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:11,920 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:11,920 | ^ 2025-09-09T00:53:11,920 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:11,920 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:11,920 | ^~~~~~~~ 2025-09-09T00:53:11,930 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:11,930 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:11,930 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:11,930 | ^ 2025-09-09T00:53:11,930 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:11,930 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:11,930 | ^~~~~~~~ 2025-09-09T00:53:11,940 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:11,940 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:11,940 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:11,940 | ^ 2025-09-09T00:53:11,940 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:11,940 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:11,940 | ^~~~~~~~ 2025-09-09T00:53:11,950 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:11,950 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:11,950 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:11,950 | ^ 2025-09-09T00:53:11,950 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:11,950 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:11,950 | ^~~~~~~~ 2025-09-09T00:53:12,086 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:12,087 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:12,087 from ./src/formats/rsmiformat.cpp:20: 2025-09-09T00:53:12,087 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:12,087 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:12,087 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:12,087 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:12,090 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:53:12,090 from ./src/formats/rsmiformat.cpp:17: 2025-09-09T00:53:12,090 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:12,090 131 | struct binary_function 2025-09-09T00:53:12,090 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:12,380 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:53:12,380 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:53:12,380 | ^~~~~~~~ 2025-09-09T00:53:12,380 In file included from ./src/formats/rsmiformat.cpp:21: 2025-09-09T00:53:12,380 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:53:12,380 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:53:12,380 | ^~~~~~~~ 2025-09-09T00:53:12,380 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:53:12,381 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:12,381 | ^~~~~~~~ 2025-09-09T00:53:12,381 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:53:12,381 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:53:12,381 | ^~~~~~~~ 2025-09-09T00:53:17,322 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/rsmiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:17,323 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/rsmiformat.o /tmp/ccn0yvvh.s 2025-09-09T00:53:17,330 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:17,844 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:17,844 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:17,844 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/rsmiformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/rsmiformat.' 2025-09-09T00:53:17,844 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/rxnformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/rxnformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:17,849 Using built-in specs. 2025-09-09T00:53:17,849 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:17,850 Target: arm-linux-gnueabihf 2025-09-09T00:53:17,850 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:17,850 Thread model: posix 2025-09-09T00:53:17,850 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:17,850 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:17,850 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/rxnformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:17,850 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/rxnformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase rxnformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cca8Vo12.s 2025-09-09T00:53:17,860 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:17,860 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:17,860 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:17,860 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:17,860 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:17,860 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:17,861 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:17,861 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:17,861 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:17,861 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:17,861 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:17,861 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:17,861 #include "..." search starts here: 2025-09-09T00:53:17,861 #include <...> search starts here: 2025-09-09T00:53:17,861 /usr/include/eigen3 2025-09-09T00:53:17,862 include 2025-09-09T00:53:17,862 /usr/include/python3.13 2025-09-09T00:53:17,862 /usr/include/c++/14 2025-09-09T00:53:17,862 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:17,862 /usr/include/c++/14/backward 2025-09-09T00:53:17,862 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:17,862 /usr/local/include 2025-09-09T00:53:17,863 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:17,863 /usr/include 2025-09-09T00:53:17,863 End of search list. 2025-09-09T00:53:17,882 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:19,500 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:19,500 from include/openbabel/mol.h:43, 2025-09-09T00:53:19,500 from ./src/formats/rxnformat.cpp:20: 2025-09-09T00:53:19,500 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:19,500 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:19,500 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:19,500 | ^ 2025-09-09T00:53:19,500 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:19,500 37 | # define UNUSED(x) x 2025-09-09T00:53:19,501 | ^ 2025-09-09T00:53:20,108 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:20,109 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:20,109 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:20,109 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:20,109 | ^ 2025-09-09T00:53:20,109 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:20,109 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:20,109 | ^~~~~~~~ 2025-09-09T00:53:20,113 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:20,113 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:20,114 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:20,114 | ^ 2025-09-09T00:53:20,114 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:20,114 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:20,114 | ^~~~~~~~ 2025-09-09T00:53:20,129 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:20,129 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:20,129 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:20,129 | ^ 2025-09-09T00:53:20,129 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:20,129 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:20,130 | ^~~~~~~~ 2025-09-09T00:53:20,135 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:20,135 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:20,135 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:20,135 | ^ 2025-09-09T00:53:20,135 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:20,135 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:20,135 | ^~~~~~~~ 2025-09-09T00:53:20,275 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:20,275 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:20,275 from ./src/formats/rxnformat.cpp:21: 2025-09-09T00:53:20,275 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:20,275 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:20,275 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:20,275 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:20,276 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:53:20,276 from ./src/formats/rxnformat.cpp:17: 2025-09-09T00:53:20,276 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:20,276 131 | struct binary_function 2025-09-09T00:53:20,276 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:20,566 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:53:20,566 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:53:20,566 | ^~~~~~~~ 2025-09-09T00:53:20,566 In file included from ./src/formats/rxnformat.cpp:22: 2025-09-09T00:53:20,566 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:53:20,567 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:53:20,567 | ^~~~~~~~ 2025-09-09T00:53:20,567 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:53:20,567 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:20,567 | ^~~~~~~~ 2025-09-09T00:53:20,567 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:53:20,567 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:53:20,567 | ^~~~~~~~ 2025-09-09T00:53:20,599 ./src/formats/rxnformat.cpp: In member function ‘virtual bool OpenBabel::RXNFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:53:20,599 ./src/formats/rxnformat.cpp:228:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:53:20,599 228 | for(i=0;iNumReactants();i++) 2025-09-09T00:53:20,599 | ~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:53:20,601 ./src/formats/rxnformat.cpp:235:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:53:20,601 235 | for(i=0;iNumProducts();i++) 2025-09-09T00:53:20,601 | ~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:53:24,397 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/rxnformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:24,398 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/rxnformat.o /tmp/cca8Vo12.s 2025-09-09T00:53:24,403 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:24,780 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:24,780 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:24,780 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/rxnformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/rxnformat.' 2025-09-09T00:53:24,782 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/shelxformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/shelxformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:24,785 Using built-in specs. 2025-09-09T00:53:24,786 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:24,786 Target: arm-linux-gnueabihf 2025-09-09T00:53:24,786 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:24,787 Thread model: posix 2025-09-09T00:53:24,787 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:24,787 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:24,787 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/shelxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:24,787 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/shelxformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase shelxformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc9ABN43.s 2025-09-09T00:53:24,798 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:24,798 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:24,799 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:24,799 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:24,799 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:24,799 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:24,799 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:24,799 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:24,800 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:24,800 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:24,800 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:24,800 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:24,800 #include "..." search starts here: 2025-09-09T00:53:24,800 #include <...> search starts here: 2025-09-09T00:53:24,800 /usr/include/eigen3 2025-09-09T00:53:24,800 include 2025-09-09T00:53:24,801 /usr/include/python3.13 2025-09-09T00:53:24,801 /usr/include/c++/14 2025-09-09T00:53:24,801 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:24,801 /usr/include/c++/14/backward 2025-09-09T00:53:24,801 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:24,801 /usr/local/include 2025-09-09T00:53:24,801 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:24,801 /usr/include 2025-09-09T00:53:24,802 End of search list. 2025-09-09T00:53:24,818 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:26,398 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:26,398 from include/openbabel/mol.h:43, 2025-09-09T00:53:26,398 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:26,398 from ./src/formats/shelxformat.cpp:18: 2025-09-09T00:53:26,398 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:26,399 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:26,399 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:26,399 | ^ 2025-09-09T00:53:26,399 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:26,399 37 | # define UNUSED(x) x 2025-09-09T00:53:26,399 | ^ 2025-09-09T00:53:26,933 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:26,933 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:26,933 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:26,933 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:26,933 | ^ 2025-09-09T00:53:26,933 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:26,934 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:26,934 | ^~~~~~~~ 2025-09-09T00:53:26,937 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:26,937 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:26,937 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:26,937 | ^ 2025-09-09T00:53:26,937 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:26,937 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:26,937 | ^~~~~~~~ 2025-09-09T00:53:26,951 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:26,951 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:26,951 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:26,951 | ^ 2025-09-09T00:53:26,951 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:26,952 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:26,952 | ^~~~~~~~ 2025-09-09T00:53:26,956 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:26,956 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:26,956 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:26,956 | ^ 2025-09-09T00:53:26,956 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:26,957 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:26,957 | ^~~~~~~~ 2025-09-09T00:53:27,094 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:27,094 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:27,094 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:27,094 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:27,095 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:27,095 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:27,095 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:27,095 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:53:27,095 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:53:27,095 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:53:27,095 from /usr/include/c++/14/ios:44, 2025-09-09T00:53:27,095 from /usr/include/c++/14/ostream:40, 2025-09-09T00:53:27,095 from include/openbabel/math/matrix3x3.h:24, 2025-09-09T00:53:27,096 from ./src/formats/shelxformat.cpp:17: 2025-09-09T00:53:27,096 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:27,096 131 | struct binary_function 2025-09-09T00:53:27,096 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:29,365 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/shelxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:29,365 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/shelxformat.o /tmp/cc9ABN43.s 2025-09-09T00:53:29,374 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:29,564 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:29,564 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:29,565 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/shelxformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/shelxformat.' 2025-09-09T00:53:29,565 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/siestaformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/siestaformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:29,570 Using built-in specs. 2025-09-09T00:53:29,570 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:29,570 Target: arm-linux-gnueabihf 2025-09-09T00:53:29,570 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:29,570 Thread model: posix 2025-09-09T00:53:29,570 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:29,570 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:29,570 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/siestaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:29,571 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/siestaformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase siestaformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccrdnxO2.s 2025-09-09T00:53:29,581 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:29,581 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:29,581 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:29,581 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:29,582 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:29,587 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:29,587 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:29,588 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:29,588 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:29,588 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:29,588 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:29,588 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:29,588 #include "..." search starts here: 2025-09-09T00:53:29,588 #include <...> search starts here: 2025-09-09T00:53:29,588 /usr/include/eigen3 2025-09-09T00:53:29,589 include 2025-09-09T00:53:29,589 /usr/include/python3.13 2025-09-09T00:53:29,589 /usr/include/c++/14 2025-09-09T00:53:29,589 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:29,589 /usr/include/c++/14/backward 2025-09-09T00:53:29,589 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:29,589 /usr/local/include 2025-09-09T00:53:29,589 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:29,589 /usr/include 2025-09-09T00:53:29,590 End of search list. 2025-09-09T00:53:29,610 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:31,110 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:31,110 from include/openbabel/mol.h:43, 2025-09-09T00:53:31,110 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:31,110 from ./src/formats/siestaformat.cpp:16: 2025-09-09T00:53:31,110 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:31,110 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:31,110 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:31,110 | ^ 2025-09-09T00:53:31,111 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:31,111 37 | # define UNUSED(x) x 2025-09-09T00:53:31,111 | ^ 2025-09-09T00:53:31,723 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:31,723 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:31,723 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:31,723 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:31,723 | ^ 2025-09-09T00:53:31,724 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:31,724 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:31,724 | ^~~~~~~~ 2025-09-09T00:53:31,724 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:31,724 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:31,724 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:31,724 | ^ 2025-09-09T00:53:31,724 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:31,724 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:31,725 | ^~~~~~~~ 2025-09-09T00:53:31,740 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:31,740 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:31,740 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:31,740 | ^ 2025-09-09T00:53:31,740 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:31,740 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:31,740 | ^~~~~~~~ 2025-09-09T00:53:31,750 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:31,750 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:31,750 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:31,750 | ^ 2025-09-09T00:53:31,750 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:31,750 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:31,750 | ^~~~~~~~ 2025-09-09T00:53:31,883 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:31,883 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:31,883 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:31,883 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:31,883 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:31,883 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:31,883 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:31,884 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:31,884 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:31,884 from include/openbabel/mol.h:35: 2025-09-09T00:53:31,885 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:31,885 131 | struct binary_function 2025-09-09T00:53:31,885 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:32,047 ./src/formats/siestaformat.cpp: In member function ‘virtual int OpenBabel::SIESTAFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:53:32,047 ./src/formats/siestaformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:53:32,047 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:53:32,047 | ~~~~^ 2025-09-09T00:53:32,047 ./src/formats/siestaformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:53:32,047 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:53:32,047 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:53:32,097 ./src/formats/siestaformat.cpp: In member function ‘virtual bool OpenBabel::SIESTAFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:53:32,097 ./src/formats/siestaformat.cpp:82:10: warning: variable ‘coordsAreAngstrom’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:53:32,097 82 | bool coordsAreAngstrom = false; 2025-09-09T00:53:32,097 | ^~~~~~~~~~~~~~~~~ 2025-09-09T00:53:32,097 ./src/formats/siestaformat.cpp:88:12: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:53:32,097 88 | size_t size; 2025-09-09T00:53:32,097 | ^~~~ 2025-09-09T00:53:32,098 ./src/formats/siestaformat.cpp:92:30: warning: unused variable ‘numSpecies’ [-Wunused-variable] 2025-09-09T00:53:32,098 92 | int atomicNum, numAtoms, numSpecies; 2025-09-09T00:53:32,098 | ^~~~~~~~~~ 2025-09-09T00:53:37,338 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/siestaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:37,338 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/siestaformat.o /tmp/ccrdnxO2.s 2025-09-09T00:53:37,343 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:37,784 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:37,784 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:37,784 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/siestaformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/siestaformat.' 2025-09-09T00:53:37,784 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/smileyformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/smileyformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:37,788 Using built-in specs. 2025-09-09T00:53:37,789 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:37,790 Target: arm-linux-gnueabihf 2025-09-09T00:53:37,790 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:37,790 Thread model: posix 2025-09-09T00:53:37,790 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:37,790 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:37,791 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/smileyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:37,793 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/smileyformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase smileyformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccfuaHNo.s 2025-09-09T00:53:37,805 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:37,806 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:37,806 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:37,806 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:37,807 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:37,808 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:37,808 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:37,808 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:37,808 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:37,808 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:37,809 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:37,809 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:37,809 #include "..." search starts here: 2025-09-09T00:53:37,809 #include <...> search starts here: 2025-09-09T00:53:37,810 /usr/include/eigen3 2025-09-09T00:53:37,810 include 2025-09-09T00:53:37,810 /usr/include/python3.13 2025-09-09T00:53:37,810 /usr/include/c++/14 2025-09-09T00:53:37,810 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:37,810 /usr/include/c++/14/backward 2025-09-09T00:53:37,811 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:37,811 /usr/local/include 2025-09-09T00:53:37,811 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:37,811 /usr/include 2025-09-09T00:53:37,811 End of search list. 2025-09-09T00:53:37,829 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:39,336 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:39,336 from include/openbabel/mol.h:43, 2025-09-09T00:53:39,336 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:39,336 from ./src/formats/smileyformat.cpp:15: 2025-09-09T00:53:39,336 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:39,336 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:39,336 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:39,337 | ^ 2025-09-09T00:53:39,337 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:39,337 37 | # define UNUSED(x) x 2025-09-09T00:53:39,337 | ^ 2025-09-09T00:53:39,949 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:39,949 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:39,949 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:39,949 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:39,949 | ^ 2025-09-09T00:53:39,949 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:39,949 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:39,949 | ^~~~~~~~ 2025-09-09T00:53:39,953 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:39,954 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:39,954 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:39,954 | ^ 2025-09-09T00:53:39,954 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:39,954 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:39,954 | ^~~~~~~~ 2025-09-09T00:53:39,969 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:39,969 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:39,969 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:39,969 | ^ 2025-09-09T00:53:39,970 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:39,970 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:39,970 | ^~~~~~~~ 2025-09-09T00:53:39,975 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:39,975 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:39,975 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:39,975 | ^ 2025-09-09T00:53:39,976 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:39,976 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:39,976 | ^~~~~~~~ 2025-09-09T00:53:40,115 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:40,115 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:40,115 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:40,115 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:40,115 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:40,115 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:40,115 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:40,116 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:40,116 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:40,116 from include/openbabel/mol.h:35: 2025-09-09T00:53:40,116 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:40,116 131 | struct binary_function 2025-09-09T00:53:40,117 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:40,396 In file included from ./src/formats/smileyformat.cpp:20: 2025-09-09T00:53:40,396 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setChiral(int, Smiley::Chirality, const std::vector&)’: 2025-09-09T00:53:40,396 include/formats/smiley.h:649:24: warning: unused parameter ‘index’ [-Wunused-parameter] 2025-09-09T00:53:40,396 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2025-09-09T00:53:40,397 | ~~~~^~~~~ 2025-09-09T00:53:40,397 include/formats/smiley.h:649:41: warning: unused parameter ‘chirality’ [-Wunused-parameter] 2025-09-09T00:53:40,397 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2025-09-09T00:53:40,397 | ~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:53:40,397 include/formats/smiley.h:649:76: warning: unused parameter ‘chiralNbrs’ [-Wunused-parameter] 2025-09-09T00:53:40,397 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2025-09-09T00:53:40,397 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:53:40,398 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addAtom(int, bool, int, int, int, int)’: 2025-09-09T00:53:40,398 include/formats/smiley.h:655:22: warning: unused parameter ‘element’ [-Wunused-parameter] 2025-09-09T00:53:40,398 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:53:40,398 | ~~~~^~~~~~~ 2025-09-09T00:53:40,398 include/formats/smiley.h:655:36: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2025-09-09T00:53:40,398 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:53:40,398 | ~~~~~^~~~~~~~ 2025-09-09T00:53:40,399 include/formats/smiley.h:655:50: warning: unused parameter ‘isotope’ [-Wunused-parameter] 2025-09-09T00:53:40,399 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:53:40,399 | ~~~~^~~~~~~ 2025-09-09T00:53:40,399 include/formats/smiley.h:655:63: warning: unused parameter ‘hCount’ [-Wunused-parameter] 2025-09-09T00:53:40,399 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:53:40,399 | ~~~~^~~~~~ 2025-09-09T00:53:40,400 include/formats/smiley.h:655:75: warning: unused parameter ‘charge’ [-Wunused-parameter] 2025-09-09T00:53:40,400 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:53:40,400 | ~~~~^~~~~~ 2025-09-09T00:53:40,400 include/formats/smiley.h:655:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2025-09-09T00:53:40,400 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:53:40,400 | ~~~~^~~~~~~~~ 2025-09-09T00:53:40,400 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addBond(int, int, int, bool, bool)’: 2025-09-09T00:53:40,401 include/formats/smiley.h:659:22: warning: unused parameter ‘source’ [-Wunused-parameter] 2025-09-09T00:53:40,401 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:53:40,401 | ~~~~^~~~~~ 2025-09-09T00:53:40,401 include/formats/smiley.h:659:34: warning: unused parameter ‘target’ [-Wunused-parameter] 2025-09-09T00:53:40,401 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:53:40,401 | ~~~~^~~~~~ 2025-09-09T00:53:40,401 include/formats/smiley.h:659:46: warning: unused parameter ‘order’ [-Wunused-parameter] 2025-09-09T00:53:40,401 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:53:40,402 | ~~~~^~~~~ 2025-09-09T00:53:40,402 include/formats/smiley.h:659:58: warning: unused parameter ‘isUp’ [-Wunused-parameter] 2025-09-09T00:53:40,402 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:53:40,402 | ~~~~~^~~~ 2025-09-09T00:53:40,402 include/formats/smiley.h:659:69: warning: unused parameter ‘isDown’ [-Wunused-parameter] 2025-09-09T00:53:40,402 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:53:40,402 | ~~~~~^~~~~~ 2025-09-09T00:53:40,403 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::operation(int)’: 2025-09-09T00:53:40,403 include/formats/smiley.h:667:24: warning: unused parameter ‘type’ [-Wunused-parameter] 2025-09-09T00:53:40,403 667 | void operation(int type) {} 2025-09-09T00:53:40,403 | ~~~~^~~~ 2025-09-09T00:53:40,403 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addOrganicSubsetAtom(int, bool)’: 2025-09-09T00:53:40,403 include/formats/smiley.h:671:35: warning: unused parameter ‘element’ [-Wunused-parameter] 2025-09-09T00:53:40,403 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2025-09-09T00:53:40,403 | ~~~~^~~~~~~ 2025-09-09T00:53:40,404 include/formats/smiley.h:671:49: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2025-09-09T00:53:40,404 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2025-09-09T00:53:40,404 | ~~~~~^~~~~~~~ 2025-09-09T00:53:40,404 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::atomPrimitive(int, int)’: 2025-09-09T00:53:40,404 include/formats/smiley.h:675:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2025-09-09T00:53:40,404 675 | void atomPrimitive(int type, int value) {} 2025-09-09T00:53:40,404 | ~~~~^~~~ 2025-09-09T00:53:40,404 include/formats/smiley.h:675:38: warning: unused parameter ‘value’ [-Wunused-parameter] 2025-09-09T00:53:40,405 675 | void atomPrimitive(int type, int value) {} 2025-09-09T00:53:40,405 | ~~~~^~~~~ 2025-09-09T00:53:40,405 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::bondPrimitive(int)’: 2025-09-09T00:53:40,405 include/formats/smiley.h:680:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2025-09-09T00:53:40,405 680 | void bondPrimitive(int type) {} 2025-09-09T00:53:40,405 | ~~~~^~~~ 2025-09-09T00:53:40,405 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setPrevious(int)’: 2025-09-09T00:53:40,406 include/formats/smiley.h:685:26: warning: unused parameter ‘index’ [-Wunused-parameter] 2025-09-09T00:53:40,406 685 | void setPrevious(int index) {} 2025-09-09T00:53:40,406 | ~~~~^~~~~ 2025-09-09T00:53:40,406 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::startRingBond(int)’: 2025-09-09T00:53:40,406 include/formats/smiley.h:689:28: warning: unused parameter ‘number’ [-Wunused-parameter] 2025-09-09T00:53:40,406 689 | void startRingBond(int number) {} 2025-09-09T00:53:40,406 | ~~~~^~~~~~ 2025-09-09T00:53:40,410 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::endRingBond(int, int)’: 2025-09-09T00:53:40,410 include/formats/smiley.h:693:26: warning: unused parameter ‘number’ [-Wunused-parameter] 2025-09-09T00:53:40,410 693 | void endRingBond(int number, int index) {} 2025-09-09T00:53:40,410 | ~~~~^~~~~~ 2025-09-09T00:53:40,410 include/formats/smiley.h:693:38: warning: unused parameter ‘index’ [-Wunused-parameter] 2025-09-09T00:53:40,410 693 | void endRingBond(int number, int index) {} 2025-09-09T00:53:40,410 | ~~~~^~~~~ 2025-09-09T00:53:40,520 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::addAtom(int, bool, int, int, int, int)’: 2025-09-09T00:53:40,520 ./src/formats/smileyformat.cpp:58:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2025-09-09T00:53:40,520 58 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) 2025-09-09T00:53:40,520 | ~~~~^~~~~~~~~ 2025-09-09T00:53:40,520 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::setChiral(int, Smiley::Chirality, const std::vector&)’: 2025-09-09T00:53:40,520 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘NotChiral’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,520 153 | switch (chirality) { 2025-09-09T00:53:40,520 | ^ 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH1’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH2’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL1’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL2’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP1’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP2’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP3’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB1’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB2’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,521 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB3’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB4’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB5’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB6’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB7’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB8’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB9’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB10’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB11’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB12’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,522 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB13’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB14’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB15’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB16’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB17’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB18’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB19’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB20’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH1’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH2’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH3’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,523 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH4’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH5’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH6’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH7’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH8’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH9’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH10’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH11’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH12’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH13’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH14’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,524 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH15’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH16’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH17’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH18’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH19’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH20’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH21’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH22’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH23’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH24’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,525 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH25’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,526 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH26’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,526 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH27’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,526 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH28’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,526 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH29’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,526 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH30’ not handled in switch [-Wswitch] 2025-09-09T00:53:40,570 ./src/formats/smileyformat.cpp: In member function ‘bool OpenBabel::SmileyFormat::AssignNbrAtoms(const std::vector&, OpenBabel::OBAtom*, long unsigned int&, long unsigned int&)’: 2025-09-09T00:53:40,570 ./src/formats/smileyformat.cpp:457:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:53:40,570 457 | aboveId = above ? above->GetId() : OBStereo::ImplicitRef; 2025-09-09T00:53:40,570 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:53:40,570 ./src/formats/smileyformat.cpp:458:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:53:40,570 458 | belowId = below ? below->GetId() : OBStereo::ImplicitRef; 2025-09-09T00:53:40,570 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:53:41,072 include/formats/smiley.h: In instantiation of ‘void Smiley::Parser::processStereochemistry() [with Callback = OpenBabel::OpenBabelCallback]’: 2025-09-09T00:53:41,072 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]’ 2025-09-09T00:53:41,072 2707 | processStereochemistry(); 2025-09-09T00:53:41,072 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:53:41,072 ./src/formats/smileyformat.cpp:365:19: required from here 2025-09-09T00:53:41,073 365 | parser.parse(smiles); 2025-09-09T00:53:41,073 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:53:41,073 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] 2025-09-09T00:53:41,073 2642 | if (m_chiralInfo[i].nbrs.size() != expectedValence && m_exceptions & InvalidChiralValence) 2025-09-09T00:53:41,073 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:53:41,560 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]’: 2025-09-09T00:53:41,561 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]’ 2025-09-09T00:53:41,561 2409 | m_ringBonds[m_prev].push_back(RingBondInfo(rnum, m_bondOrder, m_isUp, m_isDown, m_explicitBond, pos)); 2025-09-09T00:53:41,561 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:53:41,561 include/formats/smiley.h:2429:11: required from ‘void Smiley::Parser::parseRingBond() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:53:41,561 2429 | processRingBond(m_str[m_pos] - '0', m_pos); 2025-09-09T00:53:41,561 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:41,561 include/formats/smiley.h:2507:13: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:53:41,561 2507 | parseRingBond(); 2025-09-09T00:53:41,561 | ^~~~~~~~~~~~~ 2025-09-09T00:53:41,562 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]’ 2025-09-09T00:53:41,562 2698 | parseChain(); 2025-09-09T00:53:41,562 | ^~~~~~~~~~ 2025-09-09T00:53:41,562 ./src/formats/smileyformat.cpp:365:19: required from here 2025-09-09T00:53:41,562 365 | parser.parse(smiles); 2025-09-09T00:53:41,562 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:53:41,562 include/formats/smiley.h:986:14: warning: ‘Smiley::Parser::RingBondInfo::isExplicit’ will be initialized after [-Wreorder] 2025-09-09T00:53:41,562 986 | bool isExplicit; 2025-09-09T00:53:41,562 | ^~~~~~~~~~ 2025-09-09T00:53:41,562 include/formats/smiley.h:981:21: warning: ‘std::size_t Smiley::Parser::RingBondInfo::pos’ [-Wreorder] 2025-09-09T00:53:41,563 981 | std::size_t pos; 2025-09-09T00:53:41,563 | ^~~ 2025-09-09T00:53:41,563 include/formats/smiley.h:974:9: warning: when initialized here [-Wreorder] 2025-09-09T00:53:41,563 974 | RingBondInfo(int number_, int order_, bool isUp_, bool isDown_, 2025-09-09T00:53:41,563 | ^~~~~~~~~~~~ 2025-09-09T00:53:41,635 include/formats/smiley.h: In instantiation of ‘bool Smiley::Parser::parseCharNumber(char, int, int&, bool, bool) [with Callback = OpenBabel::OpenBabelCallback]’: 2025-09-09T00:53:41,635 include/formats/smiley.h:1988:15: required from ‘void Smiley::Parser::parseAtomExpr() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:53:41,635 1988 | if (parseCharNumber('#', AE_AtomicNumber, parsedOp, first_primitive, true)) { // true = no default value of 1 2025-09-09T00:53:41,635 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:41,635 include/formats/smiley.h:2092:11: required from ‘void Smiley::Parser::parseBracketAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:53:41,635 2092 | parseAtomExpr(); 2025-09-09T00:53:41,635 | ^~~~~~~~~~~~~ 2025-09-09T00:53:41,635 include/formats/smiley.h:2217:13: required from ‘bool Smiley::Parser::parseAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:53:41,635 2217 | parseBracketAtom(); 2025-09-09T00:53:41,636 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:53:41,636 include/formats/smiley.h:2495:16: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:53:41,636 2495 | if (!parseAtom() && m_str[m_pos] != '(') 2025-09-09T00:53:41,636 | ^~~~~~~~~ 2025-09-09T00:53:41,636 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]’ 2025-09-09T00:53:41,636 2698 | parseChain(); 2025-09-09T00:53:41,636 | ^~~~~~~~~~ 2025-09-09T00:53:41,636 ./src/formats/smileyformat.cpp:365:19: required from here 2025-09-09T00:53:41,636 365 | parser.parse(smiles); 2025-09-09T00:53:41,636 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:53:41,636 include/formats/smiley.h:1774:37: warning: unused parameter ‘noDefault’ [-Wunused-parameter] 2025-09-09T00:53:41,637 1774 | bool firstPrimitive, bool noDefault = false) 2025-09-09T00:53:41,637 | ~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:53:51,177 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/smileyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:51,178 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/smileyformat.o /tmp/ccfuaHNo.s 2025-09-09T00:53:51,184 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:52,054 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:52,054 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:52,055 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/smileyformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/smileyformat.' 2025-09-09T00:53:52,058 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/stlformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/stlformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:52,063 Using built-in specs. 2025-09-09T00:53:52,064 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:52,064 Target: arm-linux-gnueabihf 2025-09-09T00:53:52,064 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:52,064 Thread model: posix 2025-09-09T00:53:52,065 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:52,065 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:52,065 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/stlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:52,067 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/stlformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase stlformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cczVoi1e.s 2025-09-09T00:53:52,081 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:52,081 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:52,081 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:52,082 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:52,083 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:52,083 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:52,084 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:52,084 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:52,084 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:52,084 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:52,085 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:52,085 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:52,085 #include "..." search starts here: 2025-09-09T00:53:52,086 #include <...> search starts here: 2025-09-09T00:53:52,086 /usr/include/eigen3 2025-09-09T00:53:52,086 include 2025-09-09T00:53:52,086 /usr/include/python3.13 2025-09-09T00:53:52,087 /usr/include/c++/14 2025-09-09T00:53:52,087 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:52,087 /usr/include/c++/14/backward 2025-09-09T00:53:52,087 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:52,087 /usr/local/include 2025-09-09T00:53:52,088 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:52,088 /usr/include 2025-09-09T00:53:52,088 End of search list. 2025-09-09T00:53:52,108 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:53,608 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:53,609 from include/openbabel/mol.h:43, 2025-09-09T00:53:53,609 from ./src/formats/stlformat.cpp:28: 2025-09-09T00:53:53,609 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:53,609 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:53,609 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:53,609 | ^ 2025-09-09T00:53:53,609 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:53,609 37 | # define UNUSED(x) x 2025-09-09T00:53:53,609 | ^ 2025-09-09T00:53:54,224 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:54,224 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:54,224 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:54,224 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:54,224 | ^ 2025-09-09T00:53:54,225 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:54,225 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:54,225 | ^~~~~~~~ 2025-09-09T00:53:54,228 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:54,228 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:54,228 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:54,228 | ^ 2025-09-09T00:53:54,228 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:54,228 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:54,228 | ^~~~~~~~ 2025-09-09T00:53:54,242 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:54,242 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:54,242 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:54,243 | ^ 2025-09-09T00:53:54,243 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:54,243 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:54,243 | ^~~~~~~~ 2025-09-09T00:53:54,247 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:54,247 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:54,247 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:54,248 | ^ 2025-09-09T00:53:54,248 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:54,248 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:54,248 | ^~~~~~~~ 2025-09-09T00:53:54,386 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:54,386 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:54,386 from ./src/formats/stlformat.cpp:29: 2025-09-09T00:53:54,386 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:54,386 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:54,386 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:54,386 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:54,386 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:54,387 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:54,387 from include/openbabel/mol.h:35: 2025-09-09T00:53:54,387 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:54,387 131 | struct binary_function 2025-09-09T00:53:54,387 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:54,549 ./src/formats/stlformat.cpp: In member function ‘virtual int OpenBabel::STLFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:53:54,549 ./src/formats/stlformat.cpp:95:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:53:54,549 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:53:54,549 | ~~~~^ 2025-09-09T00:53:54,549 ./src/formats/stlformat.cpp:95:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:53:54,550 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:53:54,550 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:53:54,562 ./src/formats/stlformat.cpp: In function ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’: 2025-09-09T00:53:54,562 ./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] 2025-09-09T00:53:54,562 149 | for( int i=0 ; i < points.size()-2; i++ ) { 2025-09-09T00:53:54,562 | ~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:53:56,923 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/stlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:56,924 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/stlformat.o /tmp/cczVoi1e.s 2025-09-09T00:53:56,929 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:57,132 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:53:57,133 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:53:57,133 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/stlformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/stlformat.' 2025-09-09T00:53:57,134 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/svgformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/svgformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:57,138 Using built-in specs. 2025-09-09T00:53:57,139 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:57,139 Target: arm-linux-gnueabihf 2025-09-09T00:53:57,139 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:53:57,139 Thread model: posix 2025-09-09T00:53:57,139 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:57,139 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:57,139 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/svgformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:53:57,140 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/svgformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase svgformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc4ILQH4.s 2025-09-09T00:53:57,149 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:57,149 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:53:57,150 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:57,150 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:57,150 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:57,150 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:57,150 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:57,150 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:57,150 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:57,150 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:57,150 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:57,151 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:57,151 #include "..." search starts here: 2025-09-09T00:53:57,151 #include <...> search starts here: 2025-09-09T00:53:57,151 /usr/include/eigen3 2025-09-09T00:53:57,151 include 2025-09-09T00:53:57,151 /usr/include/python3.13 2025-09-09T00:53:57,151 /usr/include/c++/14 2025-09-09T00:53:57,151 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:57,151 /usr/include/c++/14/backward 2025-09-09T00:53:57,151 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:57,152 /usr/local/include 2025-09-09T00:53:57,152 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:57,152 /usr/include 2025-09-09T00:53:57,152 End of search list. 2025-09-09T00:53:57,170 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:58,696 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:58,696 from include/openbabel/mol.h:43, 2025-09-09T00:53:58,696 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:58,696 from ./src/formats/svgformat.cpp:15: 2025-09-09T00:53:58,696 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:58,696 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:58,697 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:58,697 | ^ 2025-09-09T00:53:58,697 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:58,697 37 | # define UNUSED(x) x 2025-09-09T00:53:58,697 | ^ 2025-09-09T00:53:59,307 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:59,307 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:59,307 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:59,307 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:59,308 | ^ 2025-09-09T00:53:59,308 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:59,308 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:59,308 | ^~~~~~~~ 2025-09-09T00:53:59,311 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:59,311 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:59,311 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:59,311 | ^ 2025-09-09T00:53:59,311 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:59,312 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:59,312 | ^~~~~~~~ 2025-09-09T00:53:59,325 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:59,325 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:59,326 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:59,326 | ^ 2025-09-09T00:53:59,326 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:59,326 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:59,326 | ^~~~~~~~ 2025-09-09T00:53:59,330 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:59,330 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:59,331 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:59,331 | ^ 2025-09-09T00:53:59,331 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:59,331 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:59,331 | ^~~~~~~~ 2025-09-09T00:53:59,469 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:59,469 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:59,469 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:59,469 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:59,469 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:59,469 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:59,470 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:59,470 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:59,470 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:59,470 from include/openbabel/mol.h:35: 2025-09-09T00:53:59,470 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:59,470 131 | struct binary_function 2025-09-09T00:53:59,470 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:59,890 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteChemObject(OpenBabel::OBConversion*)’: 2025-09-09T00:53:59,890 ./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] 2025-09-09T00:53:59,890 222 | bool nomore = _nmax && (_objects.size()==_nmax); 2025-09-09T00:53:59,890 | ~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:53:59,890 ./src/formats/svgformat.cpp:244:18: warning: unused variable ‘n’ [-Wunused-variable] 2025-09-09T00:53:59,890 244 | unsigned int n=0; 2025-09-09T00:53:59,890 | ^ 2025-09-09T00:53:59,891 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:53:59,891 ./src/formats/svgformat.cpp:269:8: warning: unused variable ‘ret’ [-Wunused-variable] 2025-09-09T00:53:59,891 269 | bool ret = WriteSVG(pConv,_objects); 2025-09-09T00:53:59,891 | ^~~ 2025-09-09T00:54:04,497 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/svgformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:04,498 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/svgformat.o /tmp/cc4ILQH4.s 2025-09-09T00:54:04,503 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:04,907 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:04,907 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:04,908 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/svgformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/svgformat.' 2025-09-09T00:54:04,910 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/textformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/textformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:04,914 Using built-in specs. 2025-09-09T00:54:04,915 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:04,915 Target: arm-linux-gnueabihf 2025-09-09T00:54:04,916 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:04,916 Thread model: posix 2025-09-09T00:54:04,916 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:04,916 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:04,917 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/textformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:04,918 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/textformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase textformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccGigV6k.s 2025-09-09T00:54:04,929 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:04,929 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:04,930 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:04,930 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:04,930 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:04,931 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:04,931 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:04,931 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:04,931 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:04,931 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:04,932 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:04,932 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:04,932 #include "..." search starts here: 2025-09-09T00:54:04,932 #include <...> search starts here: 2025-09-09T00:54:04,932 /usr/include/eigen3 2025-09-09T00:54:04,933 include 2025-09-09T00:54:04,933 /usr/include/python3.13 2025-09-09T00:54:04,933 /usr/include/c++/14 2025-09-09T00:54:04,933 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:04,933 /usr/include/c++/14/backward 2025-09-09T00:54:04,933 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:04,934 /usr/local/include 2025-09-09T00:54:04,934 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:04,934 /usr/include 2025-09-09T00:54:04,934 End of search list. 2025-09-09T00:54:04,954 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:06,278 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:06,278 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:06,278 from ./src/formats/textformat.cpp:14: 2025-09-09T00:54:06,278 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:06,278 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:06,278 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:06,278 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:54:06,279 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:54:06,279 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:54:06,279 from /usr/include/c++/14/ios:44, 2025-09-09T00:54:06,279 from /usr/include/c++/14/ostream:40, 2025-09-09T00:54:06,279 from /usr/include/c++/14/iostream:41, 2025-09-09T00:54:06,279 from include/openbabel/obconversion.h:24: 2025-09-09T00:54:06,279 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:06,279 131 | struct binary_function 2025-09-09T00:54:06,279 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:06,394 In file included from include/openbabel/text.h:23, 2025-09-09T00:54:06,394 from ./src/formats/textformat.cpp:15: 2025-09-09T00:54:06,394 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:06,394 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:06,395 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:06,395 | ^ 2025-09-09T00:54:06,395 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:06,395 37 | # define UNUSED(x) x 2025-09-09T00:54:06,395 | ^ 2025-09-09T00:54:07,567 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/textformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:07,568 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/textformat.o /tmp/ccGigV6k.s 2025-09-09T00:54:07,572 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:07,718 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:07,718 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:07,718 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/textformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/textformat.' 2025-09-09T00:54:07,719 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/thermoformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/thermoformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:07,724 Using built-in specs. 2025-09-09T00:54:07,724 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:07,724 Target: arm-linux-gnueabihf 2025-09-09T00:54:07,725 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:07,725 Thread model: posix 2025-09-09T00:54:07,725 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:07,725 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:07,725 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/thermoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:07,725 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/thermoformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase thermoformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc7w26O7.s 2025-09-09T00:54:07,736 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:07,737 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:07,737 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:07,737 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:07,737 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:07,737 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:07,737 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:07,738 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:07,738 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:07,738 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:07,738 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:07,738 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:07,738 #include "..." search starts here: 2025-09-09T00:54:07,739 #include <...> search starts here: 2025-09-09T00:54:07,739 /usr/include/eigen3 2025-09-09T00:54:07,739 include 2025-09-09T00:54:07,739 /usr/include/python3.13 2025-09-09T00:54:07,739 /usr/include/c++/14 2025-09-09T00:54:07,739 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:07,739 /usr/include/c++/14/backward 2025-09-09T00:54:07,740 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:07,740 /usr/local/include 2025-09-09T00:54:07,740 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:07,740 /usr/include 2025-09-09T00:54:07,740 End of search list. 2025-09-09T00:54:07,756 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:09,376 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:09,376 from include/openbabel/mol.h:43, 2025-09-09T00:54:09,376 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:09,376 from ./src/formats/thermoformat.cpp:19: 2025-09-09T00:54:09,377 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:09,377 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:09,377 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:09,377 | ^ 2025-09-09T00:54:09,377 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:09,377 37 | # define UNUSED(x) x 2025-09-09T00:54:09,377 | ^ 2025-09-09T00:54:09,990 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:09,990 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:09,990 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:09,990 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:09,991 | ^ 2025-09-09T00:54:09,991 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:09,991 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:09,991 | ^~~~~~~~ 2025-09-09T00:54:09,994 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:09,994 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:09,994 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:09,994 | ^ 2025-09-09T00:54:09,994 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:09,995 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:09,995 | ^~~~~~~~ 2025-09-09T00:54:10,008 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:10,008 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:10,009 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:10,009 | ^ 2025-09-09T00:54:10,009 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:10,009 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:10,009 | ^~~~~~~~ 2025-09-09T00:54:10,013 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:10,013 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:10,014 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:10,014 | ^ 2025-09-09T00:54:10,014 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:10,014 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:10,014 | ^~~~~~~~ 2025-09-09T00:54:10,152 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:10,152 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:10,152 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:10,153 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:10,153 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:10,153 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:10,153 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:10,153 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:54:10,153 from ./src/formats/thermoformat.cpp:17: 2025-09-09T00:54:10,153 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:10,153 131 | struct binary_function 2025-09-09T00:54:10,153 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:10,336 In file included from ./src/formats/thermoformat.cpp:20: 2025-09-09T00:54:10,336 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:10,337 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:54:10,337 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2025-09-09T00:54:10,337 | ~~~~~~~~^~~~~~ 2025-09-09T00:54:10,351 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:10,351 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:54:10,352 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2025-09-09T00:54:10,352 | ~~~~~~~~^~~~~~ 2025-09-09T00:54:13,450 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/thermoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:13,450 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/thermoformat.o /tmp/cc7w26O7.s 2025-09-09T00:54:13,455 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:13,722 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:13,723 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:13,723 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/thermoformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/thermoformat.' 2025-09-09T00:54:13,724 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/tinkerformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/tinkerformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:13,728 Using built-in specs. 2025-09-09T00:54:13,729 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:13,729 Target: arm-linux-gnueabihf 2025-09-09T00:54:13,729 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:13,729 Thread model: posix 2025-09-09T00:54:13,729 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:13,729 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:13,730 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/tinkerformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:13,730 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/tinkerformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase tinkerformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cch7dGUj.s 2025-09-09T00:54:13,741 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:13,741 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:13,741 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:13,741 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:13,741 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:13,742 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:13,742 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:13,742 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:13,742 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:13,742 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:13,742 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:13,742 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:13,742 #include "..." search starts here: 2025-09-09T00:54:13,743 #include <...> search starts here: 2025-09-09T00:54:13,743 /usr/include/eigen3 2025-09-09T00:54:13,743 include 2025-09-09T00:54:13,743 /usr/include/python3.13 2025-09-09T00:54:13,743 /usr/include/c++/14 2025-09-09T00:54:13,743 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:13,743 /usr/include/c++/14/backward 2025-09-09T00:54:13,743 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:13,743 /usr/local/include 2025-09-09T00:54:13,744 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:13,744 /usr/include 2025-09-09T00:54:13,744 End of search list. 2025-09-09T00:54:13,758 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:15,271 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:15,271 from include/openbabel/mol.h:43, 2025-09-09T00:54:15,271 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:15,271 from ./src/formats/tinkerformat.cpp:17: 2025-09-09T00:54:15,271 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:15,271 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:15,272 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:15,272 | ^ 2025-09-09T00:54:15,272 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:15,272 37 | # define UNUSED(x) x 2025-09-09T00:54:15,272 | ^ 2025-09-09T00:54:15,883 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:15,883 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:15,883 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:15,883 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:15,883 | ^ 2025-09-09T00:54:15,883 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:15,884 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:15,884 | ^~~~~~~~ 2025-09-09T00:54:15,887 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:15,887 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:15,887 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:15,887 | ^ 2025-09-09T00:54:15,887 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:15,887 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:15,887 | ^~~~~~~~ 2025-09-09T00:54:15,901 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:15,901 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:15,901 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:15,901 | ^ 2025-09-09T00:54:15,902 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:15,902 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:15,902 | ^~~~~~~~ 2025-09-09T00:54:15,906 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:15,906 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:15,906 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:15,906 | ^ 2025-09-09T00:54:15,907 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:15,907 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:15,907 | ^~~~~~~~ 2025-09-09T00:54:16,045 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:16,045 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:16,045 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:16,045 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:16,045 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:16,045 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:16,045 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:16,045 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:54:16,046 from /usr/include/c++/14/vector:68, 2025-09-09T00:54:16,046 from include/openbabel/mol.h:35: 2025-09-09T00:54:16,046 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:16,046 131 | struct binary_function 2025-09-09T00:54:16,046 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:16,220 In file included from include/openbabel/forcefield.h:33, 2025-09-09T00:54:16,220 from ./src/formats/tinkerformat.cpp:18: 2025-09-09T00:54:16,220 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:54:16,220 55 | virtual void Init(OBMol &box); 2025-09-09T00:54:16,220 | ^~~~ 2025-09-09T00:54:16,220 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:54:16,220 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:54:16,220 | ^~~~ 2025-09-09T00:54:16,230 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:54:16,230 229 | virtual const std::string &GetValue() const 2025-09-09T00:54:16,230 | ^~~~~~~~ 2025-09-09T00:54:16,230 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:54:16,230 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:54:16,230 76 | double GetValue (vector3 pos) const; 2025-09-09T00:54:16,230 | ^~~~~~~~ 2025-09-09T00:54:16,280 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:54:16,280 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,280 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,280 | ^ 2025-09-09T00:54:16,280 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,280 37 | # define UNUSED(x) x 2025-09-09T00:54:16,280 | ^ 2025-09-09T00:54:16,280 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:54:16,280 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,281 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,281 | ^ 2025-09-09T00:54:16,281 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,281 37 | # define UNUSED(x) x 2025-09-09T00:54:16,281 | ^ 2025-09-09T00:54:16,281 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:54:16,281 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,281 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,281 | ^ 2025-09-09T00:54:16,281 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,281 37 | # define UNUSED(x) x 2025-09-09T00:54:16,281 | ^ 2025-09-09T00:54:16,282 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:54:16,282 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,282 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,282 | ^ 2025-09-09T00:54:16,282 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,282 37 | # define UNUSED(x) x 2025-09-09T00:54:16,282 | ^ 2025-09-09T00:54:16,282 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:54:16,282 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,282 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,283 | ^ 2025-09-09T00:54:16,283 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,283 37 | # define UNUSED(x) x 2025-09-09T00:54:16,283 | ^ 2025-09-09T00:54:16,283 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:54:16,283 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,283 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,283 | ^ 2025-09-09T00:54:16,283 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,283 37 | # define UNUSED(x) x 2025-09-09T00:54:16,284 | ^ 2025-09-09T00:54:16,284 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:54:16,284 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,284 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,284 | ^ 2025-09-09T00:54:16,284 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,284 37 | # define UNUSED(x) x 2025-09-09T00:54:16,284 | ^ 2025-09-09T00:54:16,284 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:54:16,284 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:54:16,285 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:54:16,285 | ^ 2025-09-09T00:54:16,285 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:16,285 37 | # define UNUSED(x) x 2025-09-09T00:54:16,285 | ^ 2025-09-09T00:54:16,300 ./src/formats/tinkerformat.cpp: In member function ‘virtual bool OpenBabel::TinkerFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:54:16,300 ./src/formats/tinkerformat.cpp:101:9: warning: unused variable ‘atomicNum’ [-Wunused-variable] 2025-09-09T00:54:16,300 101 | int atomicNum; 2025-09-09T00:54:16,300 | ^~~~~~~~~ 2025-09-09T00:54:16,302 ./src/formats/tinkerformat.cpp: In function ‘int OpenBabel::SetMM3Type(OBAtom*)’: 2025-09-09T00:54:16,302 ./src/formats/tinkerformat.cpp:377:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:54:16,302 377 | if (b->GetHyb() == 2) // S=C 2025-09-09T00:54:16,302 | ^~ 2025-09-09T00:54:16,302 ./src/formats/tinkerformat.cpp:378:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:54:16,303 378 | countNeighborC++; break; 2025-09-09T00:54:16,303 | ^~~~~ 2025-09-09T00:54:16,304 ./src/formats/tinkerformat.cpp:220:17: warning: unused variable ‘c’ [-Wunused-variable] 2025-09-09T00:54:16,304 220 | OBAtom *b, *c; // neighbors 2025-09-09T00:54:16,304 | ^ 2025-09-09T00:54:18,825 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/tinkerformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:18,825 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/tinkerformat.o /tmp/cch7dGUj.s 2025-09-09T00:54:18,830 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:19,073 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:19,073 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:19,073 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/tinkerformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/tinkerformat.' 2025-09-09T00:54:19,074 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/titleformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/titleformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:19,078 Using built-in specs. 2025-09-09T00:54:19,079 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:19,079 Target: arm-linux-gnueabihf 2025-09-09T00:54:19,079 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:19,079 Thread model: posix 2025-09-09T00:54:19,080 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:19,080 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:19,080 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/titleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:19,082 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/titleformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase titleformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccpoqkcS.s 2025-09-09T00:54:19,092 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:19,092 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:19,092 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:19,093 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:19,093 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:19,094 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:19,094 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:19,094 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:19,094 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:19,094 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:19,095 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:19,095 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:19,095 #include "..." search starts here: 2025-09-09T00:54:19,095 #include <...> search starts here: 2025-09-09T00:54:19,095 /usr/include/eigen3 2025-09-09T00:54:19,096 include 2025-09-09T00:54:19,096 /usr/include/python3.13 2025-09-09T00:54:19,096 /usr/include/c++/14 2025-09-09T00:54:19,096 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:19,096 /usr/include/c++/14/backward 2025-09-09T00:54:19,097 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:19,097 /usr/local/include 2025-09-09T00:54:19,097 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:19,097 /usr/include 2025-09-09T00:54:19,097 End of search list. 2025-09-09T00:54:19,119 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:20,620 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:20,620 from include/openbabel/mol.h:43, 2025-09-09T00:54:20,620 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:20,620 from ./src/formats/titleformat.cpp:19: 2025-09-09T00:54:20,620 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:20,620 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:20,621 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:20,621 | ^ 2025-09-09T00:54:20,621 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:20,621 37 | # define UNUSED(x) x 2025-09-09T00:54:20,621 | ^ 2025-09-09T00:54:21,233 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:21,234 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:21,234 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:21,234 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:21,234 | ^ 2025-09-09T00:54:21,234 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:21,234 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:21,234 | ^~~~~~~~ 2025-09-09T00:54:21,238 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:21,238 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:21,239 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:21,239 | ^ 2025-09-09T00:54:21,239 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:21,239 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:21,239 | ^~~~~~~~ 2025-09-09T00:54:21,254 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:21,254 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:21,254 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:21,254 | ^ 2025-09-09T00:54:21,254 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:21,254 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:21,254 | ^~~~~~~~ 2025-09-09T00:54:21,260 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:21,260 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:21,260 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:21,260 | ^ 2025-09-09T00:54:21,260 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:21,260 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:21,260 | ^~~~~~~~ 2025-09-09T00:54:21,399 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:21,399 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:21,399 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:21,399 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:21,399 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:21,399 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:21,400 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:21,400 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:54:21,400 from /usr/include/c++/14/vector:68, 2025-09-09T00:54:21,401 from include/openbabel/mol.h:35: 2025-09-09T00:54:21,401 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:21,401 131 | struct binary_function 2025-09-09T00:54:21,401 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:23,363 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/titleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:23,363 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/titleformat.o /tmp/ccpoqkcS.s 2025-09-09T00:54:23,368 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:23,517 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:23,518 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:23,518 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/titleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/titleformat.' 2025-09-09T00:54:23,519 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/turbomoleformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/turbomoleformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:23,523 Using built-in specs. 2025-09-09T00:54:23,524 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:23,524 Target: arm-linux-gnueabihf 2025-09-09T00:54:23,524 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:23,524 Thread model: posix 2025-09-09T00:54:23,524 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:23,524 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:23,525 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/turbomoleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:23,525 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/turbomoleformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase turbomoleformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cceFiTr6.s 2025-09-09T00:54:23,535 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:23,536 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:23,536 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:23,536 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:23,536 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:23,536 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:23,536 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:23,537 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:23,537 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:23,537 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:23,537 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:23,537 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:23,537 #include "..." search starts here: 2025-09-09T00:54:23,537 #include <...> search starts here: 2025-09-09T00:54:23,538 /usr/include/eigen3 2025-09-09T00:54:23,538 include 2025-09-09T00:54:23,538 /usr/include/python3.13 2025-09-09T00:54:23,538 /usr/include/c++/14 2025-09-09T00:54:23,538 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:23,538 /usr/include/c++/14/backward 2025-09-09T00:54:23,538 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:23,538 /usr/local/include 2025-09-09T00:54:23,539 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:23,539 /usr/include 2025-09-09T00:54:23,539 End of search list. 2025-09-09T00:54:23,554 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:25,061 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:25,061 from include/openbabel/mol.h:43, 2025-09-09T00:54:25,062 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:25,062 from ./src/formats/turbomoleformat.cpp:18: 2025-09-09T00:54:25,062 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:25,062 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:25,062 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:25,062 | ^ 2025-09-09T00:54:25,062 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:25,062 37 | # define UNUSED(x) x 2025-09-09T00:54:25,062 | ^ 2025-09-09T00:54:25,673 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:25,673 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:25,673 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:25,673 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:25,673 | ^ 2025-09-09T00:54:25,673 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:25,673 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:25,673 | ^~~~~~~~ 2025-09-09T00:54:25,676 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:25,677 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:25,677 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:25,677 | ^ 2025-09-09T00:54:25,677 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:25,677 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:25,677 | ^~~~~~~~ 2025-09-09T00:54:25,691 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:25,691 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:25,691 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:25,691 | ^ 2025-09-09T00:54:25,691 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:25,691 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:25,691 | ^~~~~~~~ 2025-09-09T00:54:25,696 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:25,696 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:25,696 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:25,696 | ^ 2025-09-09T00:54:25,696 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:25,696 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:25,697 | ^~~~~~~~ 2025-09-09T00:54:25,834 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:25,834 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:25,835 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:25,835 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:25,835 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:25,835 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:25,835 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:25,835 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:54:25,835 from /usr/include/c++/14/vector:68, 2025-09-09T00:54:25,835 from include/openbabel/mol.h:35: 2025-09-09T00:54:25,835 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:25,836 131 | struct binary_function 2025-09-09T00:54:25,836 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:27,992 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/turbomoleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:27,993 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/turbomoleformat.o /tmp/cceFiTr6.s 2025-09-09T00:54:28,000 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:28,166 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:28,166 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:28,166 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/turbomoleformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/turbomoleformat.' 2025-09-09T00:54:28,166 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/unichemformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/unichemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:28,171 Using built-in specs. 2025-09-09T00:54:28,171 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:28,171 Target: arm-linux-gnueabihf 2025-09-09T00:54:28,172 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:28,172 Thread model: posix 2025-09-09T00:54:28,172 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:28,172 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:28,172 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/unichemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:28,172 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/unichemformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase unichemformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccQZMB6J.s 2025-09-09T00:54:28,184 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:28,184 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:28,184 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:28,184 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:28,185 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:28,185 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:28,185 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:28,185 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:28,185 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:28,185 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:28,185 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:28,185 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:28,186 #include "..." search starts here: 2025-09-09T00:54:28,186 #include <...> search starts here: 2025-09-09T00:54:28,186 /usr/include/eigen3 2025-09-09T00:54:28,186 include 2025-09-09T00:54:28,186 /usr/include/python3.13 2025-09-09T00:54:28,186 /usr/include/c++/14 2025-09-09T00:54:28,186 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:28,186 /usr/include/c++/14/backward 2025-09-09T00:54:28,186 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:28,186 /usr/local/include 2025-09-09T00:54:28,187 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:28,187 /usr/include 2025-09-09T00:54:28,187 End of search list. 2025-09-09T00:54:28,200 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:29,705 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:29,705 from include/openbabel/mol.h:43, 2025-09-09T00:54:29,705 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:29,705 from ./src/formats/unichemformat.cpp:17: 2025-09-09T00:54:29,705 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:29,706 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:29,706 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:29,706 | ^ 2025-09-09T00:54:29,706 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:29,706 37 | # define UNUSED(x) x 2025-09-09T00:54:29,706 | ^ 2025-09-09T00:54:30,317 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:30,317 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:30,317 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:30,317 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:30,318 | ^ 2025-09-09T00:54:30,318 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:30,318 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:30,318 | ^~~~~~~~ 2025-09-09T00:54:30,322 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:30,322 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:30,322 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:30,322 | ^ 2025-09-09T00:54:30,323 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:30,323 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:30,323 | ^~~~~~~~ 2025-09-09T00:54:30,337 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:30,337 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:30,338 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:30,338 | ^ 2025-09-09T00:54:30,338 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:30,338 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:30,338 | ^~~~~~~~ 2025-09-09T00:54:30,343 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:30,343 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:30,344 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:30,344 | ^ 2025-09-09T00:54:30,344 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:30,344 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:30,344 | ^~~~~~~~ 2025-09-09T00:54:30,483 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:30,483 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:30,483 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:30,483 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:30,483 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:30,483 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:30,483 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:30,484 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:54:30,484 from /usr/include/c++/14/vector:68, 2025-09-09T00:54:30,484 from include/openbabel/mol.h:35: 2025-09-09T00:54:30,485 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:30,485 131 | struct binary_function 2025-09-09T00:54:30,485 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:32,754 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/unichemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:32,756 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/unichemformat.o /tmp/ccQZMB6J.s 2025-09-09T00:54:32,764 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:32,948 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:32,949 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:32,949 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/unichemformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/unichemformat.' 2025-09-09T00:54:32,951 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/vaspformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/vaspformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:32,955 Using built-in specs. 2025-09-09T00:54:32,956 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:32,956 Target: arm-linux-gnueabihf 2025-09-09T00:54:32,957 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:32,957 Thread model: posix 2025-09-09T00:54:32,957 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:32,957 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:32,957 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/vaspformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:32,959 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/vaspformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase vaspformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cclnX4QA.s 2025-09-09T00:54:32,972 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:32,973 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:32,973 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:32,973 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:32,975 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:32,975 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:32,976 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:32,976 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:32,976 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:32,976 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:32,977 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:32,977 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:32,977 #include "..." search starts here: 2025-09-09T00:54:32,977 #include <...> search starts here: 2025-09-09T00:54:32,977 /usr/include/eigen3 2025-09-09T00:54:32,978 include 2025-09-09T00:54:32,978 /usr/include/python3.13 2025-09-09T00:54:32,978 /usr/include/c++/14 2025-09-09T00:54:32,978 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:32,978 /usr/include/c++/14/backward 2025-09-09T00:54:32,978 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:32,979 /usr/local/include 2025-09-09T00:54:32,979 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:32,979 /usr/include 2025-09-09T00:54:32,979 End of search list. 2025-09-09T00:54:32,997 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:34,520 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:34,520 from include/openbabel/mol.h:43, 2025-09-09T00:54:34,520 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:34,520 from ./src/formats/vaspformat.cpp:16: 2025-09-09T00:54:34,521 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:34,521 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:34,521 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:34,521 | ^ 2025-09-09T00:54:34,521 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:34,521 37 | # define UNUSED(x) x 2025-09-09T00:54:34,521 | ^ 2025-09-09T00:54:35,132 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:35,132 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:35,132 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:35,132 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:35,132 | ^ 2025-09-09T00:54:35,133 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:35,133 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:35,133 | ^~~~~~~~ 2025-09-09T00:54:35,137 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:35,137 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:35,137 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:35,137 | ^ 2025-09-09T00:54:35,137 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:35,137 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:35,137 | ^~~~~~~~ 2025-09-09T00:54:35,152 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:35,152 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:35,152 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:35,153 | ^ 2025-09-09T00:54:35,153 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:35,153 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:35,153 | ^~~~~~~~ 2025-09-09T00:54:35,158 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:35,158 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:35,158 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:35,158 | ^ 2025-09-09T00:54:35,159 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:35,159 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:35,159 | ^~~~~~~~ 2025-09-09T00:54:35,297 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:35,298 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:35,298 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:35,298 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:35,298 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:35,298 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:35,298 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:35,299 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:54:35,299 from /usr/include/c++/14/vector:68, 2025-09-09T00:54:35,299 from include/openbabel/mol.h:35: 2025-09-09T00:54:35,299 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:35,299 131 | struct binary_function 2025-09-09T00:54:35,299 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:35,648 ./src/formats/vaspformat.cpp: In member function ‘virtual int OpenBabel::VASPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:54:35,648 ./src/formats/vaspformat.cpp:111:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:54:35,648 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:54:35,648 | ~~~~^ 2025-09-09T00:54:35,648 ./src/formats/vaspformat.cpp:111:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:54:35,648 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:54:35,649 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:54:35,687 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:54:35,687 ./src/formats/vaspformat.cpp:438:17: warning: unused variable ‘freqnum’ [-Wunused-variable] 2025-09-09T00:54:35,687 438 | int freqnum = atoi(vs[0].c_str()); 2025-09-09T00:54:35,687 | ^~~~~~~ 2025-09-09T00:54:35,692 ./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] 2025-09-09T00:54:35,692 522 | std::bind2nd(std::not_equal_to(), 0.0)); 2025-09-09T00:54:35,692 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:54:35,692 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:54:35,692 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:54:35,692 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:54:35,693 | ^~~~~~~ 2025-09-09T00:54:35,702 ./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] 2025-09-09T00:54:35,702 576 | std::bind2nd(std::divides(), max / 100.0)); 2025-09-09T00:54:35,702 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:54:35,702 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:54:35,702 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:54:35,703 | ^~~~~~~ 2025-09-09T00:54:35,715 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:54:35,716 ./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] 2025-09-09T00:54:35,716 657 | for(int i = 0; i < atoms_sorted.size(); i++) 2025-09-09T00:54:35,716 | ~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:54:35,724 ./src/formats/vaspformat.cpp:668:34: warning: suggest braces around empty body in an ‘if’ statement [-Wempty-body] 2025-09-09T00:54:35,724 668 | if(atomicNums.size() > 0); 2025-09-09T00:54:35,724 | ^ 2025-09-09T00:54:35,725 ./src/formats/vaspformat.cpp:668:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:54:35,725 668 | if(atomicNums.size() > 0); 2025-09-09T00:54:35,725 | ^~ 2025-09-09T00:54:35,725 ./src/formats/vaspformat.cpp:669:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:54:35,725 669 | atomicNums.rbegin()->second++; 2025-09-09T00:54:35,725 | ^~~~~~~~~~ 2025-09-09T00:54:41,634 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:54:41,634 ./src/formats/vaspformat.cpp:397:21: warning: ‘fermi’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:54:41,635 397 | dos->SetData(fermi, energies, densities, integration); 2025-09-09T00:54:41,635 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:54:41,635 ./src/formats/vaspformat.cpp:379:14: note: ‘fermi’ was declared here 2025-09-09T00:54:41,635 379 | double fermi; 2025-09-09T00:54:41,635 | ^~~~~ 2025-09-09T00:54:41,635 ./src/formats/vaspformat.cpp:543:14: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:54:41,635 543 | double en_kcal_per_mole = enthalpy_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:54:41,635 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:54:41,636 ./src/formats/vaspformat.cpp:158:12: note: ‘enthalpy_eV’ was declared here 2025-09-09T00:54:41,636 158 | double enthalpy_eV, pv_eV; 2025-09-09T00:54:41,636 | ^~~~~~~~~~~ 2025-09-09T00:54:41,636 ./src/formats/vaspformat.cpp:544:14: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:54:41,636 544 | double pv_kcal_per_mole = pv_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:54:41,636 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:54:41,636 ./src/formats/vaspformat.cpp:158:25: note: ‘pv_eV’ was declared here 2025-09-09T00:54:41,636 158 | double enthalpy_eV, pv_eV; 2025-09-09T00:54:41,636 | ^~~~~ 2025-09-09T00:54:47,888 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:54:47,888 ./src/formats/vaspformat.cpp:752:26: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:54:47,888 752 | if (atom->HasData("move")) { 2025-09-09T00:54:47,888 | ~~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:54:47,888 ./src/formats/vaspformat.cpp:726:13: note: ‘atom’ was declared here 2025-09-09T00:54:47,888 726 | OBAtom *atom; 2025-09-09T00:54:47,888 | ^~~~ 2025-09-09T00:54:49,043 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/vaspformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:49,043 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/vaspformat.o /tmp/cclnX4QA.s 2025-09-09T00:54:49,048 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:50,277 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:50,277 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:50,277 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/vaspformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/vaspformat.' 2025-09-09T00:54:50,278 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/viewmolformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/viewmolformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:50,282 Using built-in specs. 2025-09-09T00:54:50,282 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:50,283 Target: arm-linux-gnueabihf 2025-09-09T00:54:50,283 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:50,283 Thread model: posix 2025-09-09T00:54:50,283 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:50,283 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:50,283 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/viewmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:50,283 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/viewmolformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase viewmolformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/cc7HFzI4.s 2025-09-09T00:54:50,294 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:50,295 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:50,295 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:50,295 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:50,295 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:50,295 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:50,296 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:50,296 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:50,296 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:50,296 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:50,296 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:50,296 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:50,297 #include "..." search starts here: 2025-09-09T00:54:50,297 #include <...> search starts here: 2025-09-09T00:54:50,297 /usr/include/eigen3 2025-09-09T00:54:50,297 include 2025-09-09T00:54:50,297 /usr/include/python3.13 2025-09-09T00:54:50,297 /usr/include/c++/14 2025-09-09T00:54:50,297 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:50,298 /usr/include/c++/14/backward 2025-09-09T00:54:50,298 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:50,298 /usr/local/include 2025-09-09T00:54:50,298 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:50,298 /usr/include 2025-09-09T00:54:50,298 End of search list. 2025-09-09T00:54:50,316 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:51,836 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:51,837 from include/openbabel/mol.h:43, 2025-09-09T00:54:51,837 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:51,837 from ./src/formats/viewmolformat.cpp:17: 2025-09-09T00:54:51,837 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:51,837 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:51,837 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:51,837 | ^ 2025-09-09T00:54:51,837 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:51,837 37 | # define UNUSED(x) x 2025-09-09T00:54:51,838 | ^ 2025-09-09T00:54:52,453 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:52,453 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:52,454 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:52,454 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:52,454 | ^ 2025-09-09T00:54:52,454 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:52,454 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:52,454 | ^~~~~~~~ 2025-09-09T00:54:52,458 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:52,458 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:52,458 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:52,458 | ^ 2025-09-09T00:54:52,458 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:52,458 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:52,458 | ^~~~~~~~ 2025-09-09T00:54:52,473 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:52,474 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:52,474 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:52,474 | ^ 2025-09-09T00:54:52,474 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:52,474 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:52,474 | ^~~~~~~~ 2025-09-09T00:54:52,478 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:52,479 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:52,479 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:52,479 | ^ 2025-09-09T00:54:52,479 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:52,479 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:52,479 | ^~~~~~~~ 2025-09-09T00:54:52,617 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:52,617 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:52,617 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:52,617 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:52,618 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:52,618 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:52,618 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:52,618 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:54:52,618 from /usr/include/c++/14/vector:68, 2025-09-09T00:54:52,618 from include/openbabel/mol.h:35: 2025-09-09T00:54:52,618 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:52,618 131 | struct binary_function 2025-09-09T00:54:52,618 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:54,929 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/viewmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:54,929 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/viewmolformat.o /tmp/cc7HFzI4.s 2025-09-09T00:54:54,934 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:55,109 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:55,109 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:55,110 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/viewmolformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/viewmolformat.' 2025-09-09T00:54:55,111 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/xedformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/xedformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:55,116 Using built-in specs. 2025-09-09T00:54:55,117 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:55,117 Target: arm-linux-gnueabihf 2025-09-09T00:54:55,117 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:55,117 Thread model: posix 2025-09-09T00:54:55,117 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:55,117 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:55,117 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/xedformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:55,118 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/xedformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase xedformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccXYvxir.s 2025-09-09T00:54:55,128 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:55,128 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:55,128 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:55,128 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:55,128 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:55,129 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:55,129 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:55,129 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:55,129 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:55,129 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:55,129 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:55,129 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:55,130 #include "..." search starts here: 2025-09-09T00:54:55,130 #include <...> search starts here: 2025-09-09T00:54:55,130 /usr/include/eigen3 2025-09-09T00:54:55,130 include 2025-09-09T00:54:55,130 /usr/include/python3.13 2025-09-09T00:54:55,130 /usr/include/c++/14 2025-09-09T00:54:55,130 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:55,130 /usr/include/c++/14/backward 2025-09-09T00:54:55,130 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:55,130 /usr/local/include 2025-09-09T00:54:55,130 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:55,131 /usr/include 2025-09-09T00:54:55,131 End of search list. 2025-09-09T00:54:55,149 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:54:56,652 In file included from include/openbabel/atom.h:33, 2025-09-09T00:54:56,653 from include/openbabel/mol.h:43, 2025-09-09T00:54:56,653 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:54:56,653 from ./src/formats/xedformat.cpp:17: 2025-09-09T00:54:56,653 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:54:56,653 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:54:56,653 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:54:56,653 | ^ 2025-09-09T00:54:56,653 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:54:56,653 37 | # define UNUSED(x) x 2025-09-09T00:54:56,654 | ^ 2025-09-09T00:54:57,264 In file included from include/openbabel/mol.h:52: 2025-09-09T00:54:57,264 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:57,265 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:57,265 862 | {return new OBVibrationData(*this);} 2025-09-09T00:54:57,265 | ^ 2025-09-09T00:54:57,265 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:54:57,265 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:54:57,265 | ^~~~~~~~ 2025-09-09T00:54:57,268 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:57,268 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:57,268 907 | {return new OBDOSData(*this);} 2025-09-09T00:54:57,269 | ^ 2025-09-09T00:54:57,269 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:54:57,269 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:54:57,269 | ^~~~~~~~ 2025-09-09T00:54:57,282 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:57,283 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:57,283 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:54:57,283 | ^ 2025-09-09T00:54:57,283 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:54:57,283 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:54:57,283 | ^~~~~~~~ 2025-09-09T00:54:57,287 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:54:57,288 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:54:57,288 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:54:57,288 | ^ 2025-09-09T00:54:57,288 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:54:57,288 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:54:57,288 | ^~~~~~~~ 2025-09-09T00:54:57,426 In file included from include/openbabel/format.h:22, 2025-09-09T00:54:57,426 from include/openbabel/obconversion.h:37, 2025-09-09T00:54:57,426 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:54:57,426 include/openbabel/plugin.h: At global scope: 2025-09-09T00:54:57,427 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:54:57,427 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:54:57,427 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:57,427 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:54:57,427 from /usr/include/c++/14/vector:68, 2025-09-09T00:54:57,427 from include/openbabel/mol.h:35: 2025-09-09T00:54:57,427 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:54:57,427 131 | struct binary_function 2025-09-09T00:54:57,427 | ^~~~~~~~~~~~~~~ 2025-09-09T00:54:59,531 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/xedformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:59,532 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/xedformat.o /tmp/ccXYvxir.s 2025-09-09T00:54:59,536 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:54:59,698 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:54:59,698 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:54:59,698 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/xedformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/xedformat.' 2025-09-09T00:54:59,700 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/xsfformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/xsfformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:54:59,703 Using built-in specs. 2025-09-09T00:54:59,704 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:54:59,704 Target: arm-linux-gnueabihf 2025-09-09T00:54:59,704 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:54:59,705 Thread model: posix 2025-09-09T00:54:59,705 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:54:59,705 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:54:59,705 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/xsfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:54:59,705 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/xsfformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase xsfformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccAIZBpZ.s 2025-09-09T00:54:59,715 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:54:59,716 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:54:59,716 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:54:59,716 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:54:59,716 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:54:59,716 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:54:59,716 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:54:59,716 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:54:59,716 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:54:59,717 ignoring duplicate directory "/usr/include/" 2025-09-09T00:54:59,717 as it is a non-system directory that duplicates a system directory 2025-09-09T00:54:59,717 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:54:59,717 #include "..." search starts here: 2025-09-09T00:54:59,717 #include <...> search starts here: 2025-09-09T00:54:59,717 /usr/include/eigen3 2025-09-09T00:54:59,717 include 2025-09-09T00:54:59,717 /usr/include/python3.13 2025-09-09T00:54:59,717 /usr/include/c++/14 2025-09-09T00:54:59,717 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:54:59,717 /usr/include/c++/14/backward 2025-09-09T00:54:59,718 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:54:59,718 /usr/local/include 2025-09-09T00:54:59,718 /usr/include/arm-linux-gnueabihf 2025-09-09T00:54:59,718 /usr/include 2025-09-09T00:54:59,718 End of search list. 2025-09-09T00:54:59,733 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:55:01,245 In file included from include/openbabel/atom.h:33, 2025-09-09T00:55:01,245 from include/openbabel/mol.h:43, 2025-09-09T00:55:01,246 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:55:01,246 from ./src/formats/xsfformat.cpp:16: 2025-09-09T00:55:01,246 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:55:01,246 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:55:01,246 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:55:01,246 | ^ 2025-09-09T00:55:01,246 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:55:01,246 37 | # define UNUSED(x) x 2025-09-09T00:55:01,246 | ^ 2025-09-09T00:55:01,858 In file included from include/openbabel/mol.h:52: 2025-09-09T00:55:01,859 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:55:01,859 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:55:01,859 862 | {return new OBVibrationData(*this);} 2025-09-09T00:55:01,859 | ^ 2025-09-09T00:55:01,859 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:55:01,859 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:55:01,859 | ^~~~~~~~ 2025-09-09T00:55:01,862 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:55:01,863 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:55:01,863 907 | {return new OBDOSData(*this);} 2025-09-09T00:55:01,863 | ^ 2025-09-09T00:55:01,863 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:55:01,863 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:55:01,863 | ^~~~~~~~ 2025-09-09T00:55:01,877 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:55:01,877 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:55:01,877 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:55:01,877 | ^ 2025-09-09T00:55:01,877 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:55:01,877 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:55:01,878 | ^~~~~~~~ 2025-09-09T00:55:01,882 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:55:01,882 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:55:01,882 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:55:01,882 | ^ 2025-09-09T00:55:01,882 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:55:01,883 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:55:01,883 | ^~~~~~~~ 2025-09-09T00:55:02,021 In file included from include/openbabel/format.h:22, 2025-09-09T00:55:02,021 from include/openbabel/obconversion.h:37, 2025-09-09T00:55:02,021 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:55:02,021 include/openbabel/plugin.h: At global scope: 2025-09-09T00:55:02,022 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:55:02,022 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:55:02,022 | ^~~~~~~~~~~~~~~ 2025-09-09T00:55:02,022 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:55:02,022 from /usr/include/c++/14/vector:68, 2025-09-09T00:55:02,022 from include/openbabel/mol.h:35: 2025-09-09T00:55:02,022 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:55:02,022 131 | struct binary_function 2025-09-09T00:55:02,022 | ^~~~~~~~~~~~~~~ 2025-09-09T00:55:04,777 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/xsfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:55:04,777 as -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -march=armv6+fp -mfloat-abi=hard -meabi=5 -o build/temp.linux-armv7l-cpython-313/src/formats/xsfformat.o /tmp/ccAIZBpZ.s 2025-09-09T00:55:04,782 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:55:05,010 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/14/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/ 2025-09-09T00:55:05,010 LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/14/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/14/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ 2025-09-09T00:55:05,011 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/xsfformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/xsfformat.' 2025-09-09T00:55:05,012 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/ -I/usr/include/armv7l-linux-gnu/ -I/usr/include/eigen3 -Iinclude -I/usr/include/python3.13 -c ./src/formats/xtcformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/xtcformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:55:05,017 Using built-in specs. 2025-09-09T00:55:05,017 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:55:05,017 Target: arm-linux-gnueabihf 2025-09-09T00:55:05,018 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-09T00:55:05,018 Thread model: posix 2025-09-09T00:55:05,018 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:55:05,018 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:55:05,018 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/armv7l-linux-gnu/' '-I' '/usr/include/eigen3' '-I' 'include' '-I' '/usr/include/python3.13' '-c' '-o' 'build/temp.linux-armv7l-cpython-313/src/formats/xtcformat.o' '-std=c++14' '-v' '-Wpedantic' '-Wall' '-Wextra' '-fPIC' '-O3' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'build/temp.linux-armv7l-cpython-313/src/formats/' 2025-09-09T00:55:05,018 /usr/libexec/gcc/arm-linux-gnueabihf/14/cc1plus -quiet -v -I /usr/include/ -I /usr/include/armv7l-linux-gnu/ -I /usr/include/eigen3 -I include -I /usr/include/python3.13 -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D NDEBUG ./src/formats/xtcformat.cpp -D_TIME_BITS=64 -D_FILE_OFFSET_BITS=64 -quiet -dumpdir build/temp.linux-armv7l-cpython-313/src/formats/ -dumpbase xtcformat.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -O2 -O3 -Wsign-compare -Wpedantic -Wall -Wextra -std=c++14 -version -fno-strict-overflow -fPIC -o /tmp/ccx2bL8q.s 2025-09-09T00:55:05,030 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:55:05,030 compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP 2025-09-09T00:55:05,030 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:55:05,030 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:55:05,030 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:55:05,031 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:55:05,031 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:55:05,031 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:55:05,031 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:55:05,031 ignoring duplicate directory "/usr/include/" 2025-09-09T00:55:05,031 as it is a non-system directory that duplicates a system directory 2025-09-09T00:55:05,031 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:55:05,031 #include "..." search starts here: 2025-09-09T00:55:05,031 #include <...> search starts here: 2025-09-09T00:55:05,032 /usr/include/eigen3 2025-09-09T00:55:05,032 include 2025-09-09T00:55:05,032 /usr/include/python3.13 2025-09-09T00:55:05,032 /usr/include/c++/14 2025-09-09T00:55:05,032 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:55:05,032 /usr/include/c++/14/backward 2025-09-09T00:55:05,032 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:55:05,033 /usr/local/include 2025-09-09T00:55:05,033 /usr/include/arm-linux-gnueabihf 2025-09-09T00:55:05,033 /usr/include 2025-09-09T00:55:05,033 End of search list. 2025-09-09T00:55:05,050 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:55:05,504 ./src/formats/xtcformat.cpp:23:10: fatal error: rpc/types.h: No such file or directory 2025-09-09T00:55:05,504 23 | #include 2025-09-09T00:55:05,505 | ^~~~~~~~~~~~~ 2025-09-09T00:55:05,505 compilation terminated. 2025-09-09T00:55:05,505 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-09T00:55:05,671 ERROR: python setup.py bdist_wheel exited with 1 2025-09-09T00:55:05,685 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-09T00:55:05,685 exec(compile('"'"''"'"''"'"' 2025-09-09T00:55:05,685 # This is -- a caller that pip uses to run setup.py 2025-09-09T00:55:05,685 # 2025-09-09T00:55:05,685 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-09T00:55:05,685 # import from `distutils.core` to work with newer packaging standards. 2025-09-09T00:55:05,685 # - It provides a clear error message when setuptools is not installed. 2025-09-09T00:55:05,685 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-09T00:55:05,685 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-09T00:55:05,685 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-09T00:55:05,685 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-09T00:55:05,685 import os, sys, tokenize, traceback 2025-09-09T00:55:05,685 2025-09-09T00:55:05,685 try: 2025-09-09T00:55:05,685 import setuptools 2025-09-09T00:55:05,685 except ImportError: 2025-09-09T00:55:05,685 print( 2025-09-09T00:55:05,685 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-09T00:55:05,685 "the build environment with exception:", 2025-09-09T00:55:05,685 file=sys.stderr, 2025-09-09T00:55:05,685 ) 2025-09-09T00:55:05,685 traceback.print_exc() 2025-09-09T00:55:05,685 sys.exit(1) 2025-09-09T00:55:05,685 2025-09-09T00:55:05,685 __file__ = %r 2025-09-09T00:55:05,685 sys.argv[0] = __file__ 2025-09-09T00:55:05,685 2025-09-09T00:55:05,685 if os.path.exists(__file__): 2025-09-09T00:55:05,685 filename = __file__ 2025-09-09T00:55:05,685 with tokenize.open(__file__) as f: 2025-09-09T00:55:05,685 setup_py_code = f.read() 2025-09-09T00:55:05,685 else: 2025-09-09T00:55:05,685 filename = "" 2025-09-09T00:55:05,685 setup_py_code = "from setuptools import setup; setup()" 2025-09-09T00:55:05,685 2025-09-09T00:55:05,685 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T00:55:05,685 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-38rab5zi/maagbel_5dfce457d0e44020bbc659fc751f0b87/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-vo9bbe93[/] 2025-09-09T00:55:05,685 [bold magenta]cwd[/]: /tmp/pip-wheel-38rab5zi/maagbel_5dfce457d0e44020bbc659fc751f0b87/ 2025-09-09T00:55:05,686 Building wheel for maagbel (setup.py): finished with status 'error' 2025-09-09T00:55:05,686 ERROR: Failed building wheel for maagbel 2025-09-09T00:55:05,687 Running setup.py clean for maagbel 2025-09-09T00:55:05,688 Running command python setup.py clean 2025-09-09T00:55:06,551 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'mail' 2025-09-09T00:55:06,551 warnings.warn(msg) 2025-09-09T00:55:06,954 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T00:55:06,954 !! 2025-09-09T00:55:06,954 ******************************************************************************** 2025-09-09T00:55:06,954 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T00:55:06,954 License :: OSI Approved :: GNU General Public License v2 (GPLv2) 2025-09-09T00:55:06,955 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T00:55:06,955 ******************************************************************************** 2025-09-09T00:55:06,955 !! 2025-09-09T00:55:06,955 self._finalize_license_expression() 2025-09-09T00:55:07,029 running clean 2025-09-09T00:55:07,101 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-09T00:55:07,167 'build/lib.linux-armv7l-cpython-313' does not exist -- can't clean it 2025-09-09T00:55:07,167 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-09T00:55:07,167 'build/scripts-3.13' does not exist -- can't clean it 2025-09-09T00:55:07,167 removing 'build' 2025-09-09T00:55:07,282 Failed to build maagbel 2025-09-09T00:55:07,283 ERROR: Failed to build one or more wheels 2025-09-09T00:55:07,283 Exception information: 2025-09-09T00:55:07,283 Traceback (most recent call last): 2025-09-09T00:55:07,283 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-09T00:55:07,283 status = _inner_run() 2025-09-09T00:55:07,283 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-09T00:55:07,283 return self.run(options, args) 2025-09-09T00:55:07,283 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-09T00:55:07,283 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-09T00:55:07,283 return func(self, options, args) 2025-09-09T00:55:07,283 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-09T00:55:07,283 raise CommandError("Failed to build one or more wheels") 2025-09-09T00:55:07,283 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-09T00:55:07,288 Removed build tracker: '/tmp/pip-build-tracker-b88b9ob_'